From ea03b06fd1dca53b2e849e516aa177d4c84bc678 Mon Sep 17 00:00:00 2001 From: Thiseas Christos Lamnidis Date: Mon, 30 Oct 2023 14:42:30 +0100 Subject: [PATCH 01/12] Added SSF for 2018_Lamnidis_Fennoscandia --- .../2018_Lamnidis_Fennoscandia.ssf | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 packages/2018_Lamnidis_Fennoscandia/2018_Lamnidis_Fennoscandia.ssf diff --git a/packages/2018_Lamnidis_Fennoscandia/2018_Lamnidis_Fennoscandia.ssf b/packages/2018_Lamnidis_Fennoscandia/2018_Lamnidis_Fennoscandia.ssf new file mode 100644 index 0000000..c26ef55 --- /dev/null +++ b/packages/2018_Lamnidis_Fennoscandia/2018_Lamnidis_Fennoscandia.ssf @@ -0,0 +1,23 @@ +poseidon_IDs udg library_built notes sample_accession study_accession run_accession sample_alias secondary_sample_accession first_public last_updated instrument_model library_layout library_source instrument_platform library_name library_strategy fastq_ftp fastq_aspera fastq_bytes fastq_md5 read_count submitted_ftp +BOO001.A0101 n/a ds n/a SAMEA5043928 PRJEB29360 ERR2857041 BOO001 ERS2855662 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA BOO001.A0101 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2857041/ERR2857041.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/001/ERR2857041/ERR2857041.fastq.gz 172101531 b0dff0511586cd267cb55908d8c4d70c 4997889 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857041/BOO001.A0101.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857041/BOO001.A0101.bam.bai +BOO003.A0101 n/a ds n/a SAMEA5043930 PRJEB29360 ERR2857043 BOO003 ERS2855664 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA BOO003.A0101 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2857043/ERR2857043.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/003/ERR2857043/ERR2857043.fastq.gz 166882210 2bc290ec218aa807285981252a335723 4578933 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857043/BOO003.A0101.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857043/BOO003.A0101.bam.bai +BOO006.A0101 n/a ds n/a SAMEA5043933 PRJEB29360 ERR2857046 BOO006 ERS2855667 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA BOO006.A0101 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2857046/ERR2857046.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/006/ERR2857046/ERR2857046.fastq.gz 159714217 1297d8e5215097d5235c0450c7613057 4376351 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857046/BOO006.A0101.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857046/BOO006.A0101.bam.bai +JK1967 n/a ds n/a SAMEA5043935 PRJEB29360 ERR2857048 JK1967 ERS2855669 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA XXX001.A171061 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2857048/ERR2857048.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/008/ERR2857048/ERR2857048.fastq.gz 3978219 8c56212f7ecab107af29a64eb3515cdc 141089 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857048/JK1967.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857048/JK1967.bam.bai +JK1968 n/a ds n/a SAMEA5043936 PRJEB29360 ERR2857049 JK1968 ERS2855670 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA XXX001.A171062 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2857049/ERR2857049.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/009/ERR2857049/ERR2857049.fastq.gz 84503779 373f663b4e65b97fce3f9b62a45ea2c5 2424594 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857049/JK1968.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857049/JK1968.bam.bai +JK1970 n/a ds n/a SAMEA5043937 PRJEB29360 ERR2857050 JK1970 ERS2855671 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA XXX001.A171063 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2857050/ERR2857050.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/000/ERR2857050/ERR2857050.fastq.gz 59585730 ffa6dc997ba777af49290caf30107929 1804933 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857050/JK1970.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857050/JK1970.bam.bai +JK2067 n/a ds n/a SAMEA5043940 PRJEB29360 ERR2857053 JK2067 ERS2855674 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA XXX001.A171066 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2857053/ERR2857053.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/003/ERR2857053/ERR2857053.fastq.gz 3639370 a0f380b6d9f2f733b4aa73ec0789c91e 125285 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857053/JK2067.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857053/JK2067.bam.bai +JK2065 n/a ds n/a SAMEA5043938 PRJEB29360 ERR2857058 JK2065 ERS2855672 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA XXX001.A16125 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2857058/ERR2857058.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/008/ERR2857058/ERR2857058.fastq.gz 571987279 181b4c3d1de17311ce54aa887b089eb7 16806633 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857058/JK2065.nU.SE.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857058/JK2065.nU.SE.bam.bai +JK1970 n/a ds n/a SAMEA5043937 PRJEB29360 ERR2857060 JK1970 ERS2855671 2018-11-27 2018-11-16 NextSeq 500 SINGLE GENOMIC ILLUMINA XXX001.A16124 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2857060/ERR2857060.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/000/ERR2857060/ERR2857060.fastq.gz 177659257 1057617b149c7b4a568d5508c43f85f8 4547175 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857060/JK1970.nU.PE.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857060/JK1970.nU.PE.bam.bai +JK2065 n/a ds n/a SAMEA5043938 PRJEB29360 ERR2857061 JK2065 ERS2855672 2018-11-27 2018-11-16 NextSeq 500 SINGLE GENOMIC ILLUMINA XXX001.A16125 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2857061/ERR2857061.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/001/ERR2857061/ERR2857061.fastq.gz 155765133 3ad5a9f216fb47fc69db249f5dca1c04 4022905 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857061/JK2065.nU.PE.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857061/JK2065.nU.PE.bam.bai +BOO002.A0101 n/a ds n/a SAMEA5043929 PRJEB29360 ERR2857042 BOO002 ERS2855663 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA BOO002.A0101 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2857042/ERR2857042.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/002/ERR2857042/ERR2857042.fastq.gz 111296254 ecf72befbbab2ba932fff5f2093bdfdf 2798785 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857042/BOO002.A0101.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857042/BOO002.A0101.bam.bai +BOO005.A0101 n/a ds n/a SAMEA5043932 PRJEB29360 ERR2857045 BOO005 ERS2855666 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA BOO005.A0101 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2857045/ERR2857045.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/005/ERR2857045/ERR2857045.fastq.gz 326775388 6ddd68cc153c9580fbb8723531d2ece9 9634975 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857045/BOO005.A0101.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857045/BOO005.A0101.bam.bai +JK2065 n/a ds n/a SAMEA5043938 PRJEB29360 ERR2857051 JK2065 ERS2855672 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA XXX001.A171064 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2857051/ERR2857051.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/001/ERR2857051/ERR2857051.fastq.gz 48338916 1ac63221ff445543cd3a49fa62265231 1524054 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857051/JK2065.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857051/JK2065.bam.bai +JK1970 n/a ds n/a SAMEA5043937 PRJEB29360 ERR2857057 JK1970 ERS2855671 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA XXX001.A16124 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2857057/ERR2857057.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/007/ERR2857057/ERR2857057.fastq.gz 610331876 1f66510c6439b7538dcdf91e9033f111 18080796 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857057/JK1970.nU.SE.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857057/JK1970.nU.SE.bam.bai +BOO004.A0101 n/a ds n/a SAMEA5043931 PRJEB29360 ERR2857044 BOO004 ERS2855665 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA BOO004.A0101 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2857044/ERR2857044.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/004/ERR2857044/ERR2857044.fastq.gz 351467229 74e0b9dd29f31d14f9d5f9f82e083d27 9840133 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857044/BOO004.A0101.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857044/BOO004.A0101.bam.bai +JK1963 n/a ds n/a SAMEA5043934 PRJEB29360 ERR2857047 JK1963 ERS2855668 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA XXX001.A171060 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2857047/ERR2857047.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/007/ERR2857047/ERR2857047.fastq.gz 5449546 ad8e4cfadde42dc2563e7e2f2764e995 173258 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857047/JK1963.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857047/JK1963.bam.bai +JK2066 n/a ds n/a SAMEA5043939 PRJEB29360 ERR2857052 JK2066 ERS2855673 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA XXX001.A171065 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2857052/ERR2857052.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/002/ERR2857052/ERR2857052.fastq.gz 4498748 14007200e4b6b65513fb73dc60206ebd 159257 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857052/JK2066.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857052/JK2066.bam.bai +CHV001.A0101 n/a ds n/a SAMEA5043941 PRJEB29360 ERR2857054 CHV001 ERS2855675 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA CHV001.A0101 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2857054/ERR2857054.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/004/ERR2857054/ERR2857054.fastq.gz 177880280 7c167608f9d493a29f7584b6a7fdff0f 4940474 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857054/CHV001.A0101.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857054/CHV001.A0101.bam.bai +CHV002.A0101 n/a ds n/a SAMEA5043942 PRJEB29360 ERR2857055 CHV002 ERS2855676 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA CHV002.A0101 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2857055/ERR2857055.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/005/ERR2857055/ERR2857055.fastq.gz 106341886 dc4e782cc8e071c7c70e2c7113cf74b0 2820563 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857055/CHV002.A0101.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857055/CHV002.A0101.bam.bai +JK1968 n/a ds n/a SAMEA5043936 PRJEB29360 ERR2857056 JK1968 ERS2855670 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA XXX001.A16123 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2857056/ERR2857056.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/006/ERR2857056/ERR2857056.fastq.gz 494908398 bbfd94a8fe91e4d6c2dfa9caf8324f79 15193613 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857056/JK1968.nU.SE.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857056/JK1968.nU.SE.bam.bai +JK1968 n/a ds n/a SAMEA5043936 PRJEB29360 ERR2857059 JK1968 ERS2855670 2018-11-27 2018-11-16 NextSeq 500 SINGLE GENOMIC ILLUMINA XXX001.A16123 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2857059/ERR2857059.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/009/ERR2857059/ERR2857059.fastq.gz 169406455 6f4ff1b7097e863adb71b0c6b5f92ab7 4454175 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857059/JK1968.nU.PE.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857059/JK1968.nU.PE.bam.bai +Saami001 plus n/a Present-day data, so no damage. Set udg to 'plus' SAMEA5043943 PRJEB29360 ERR2857062 Saami001 ERS2855677 2018-11-27 2018-11-16 Illumina Genome Analyzer II PAIRED GENOMIC ILLUMINA Saami_090511 WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2857062/ERR2857062.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2857062/ERR2857062_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2857062/ERR2857062_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/002/ERR2857062/ERR2857062.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/002/ERR2857062/ERR2857062_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/002/ERR2857062/ERR2857062_2.fastq.gz 341167554;25011768303;25286553258 3ba1e49107855df725523c4d84757c0f;230cf4747534e9d154b2a9801aa6a51b;3a1be192a3a8d7655cd4b291c5da65d5 233869444 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857062/Saami.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857062/Saami.bam.bai From d6f33098f041f6aa2049e3fc24cf5d8b60f315b1 Mon Sep 17 00:00:00 2001 From: Thiseas Christos Lamnidis Date: Thu, 18 Jul 2024 10:56:09 +0200 Subject: [PATCH 02/12] Revert "Added SSF for 2018_Lamnidis_Fennoscandia" This reverts commit ea03b06fd1dca53b2e849e516aa177d4c84bc678. --- .../2018_Lamnidis_Fennoscandia.ssf | 23 ------------------- 1 file changed, 23 deletions(-) delete mode 100644 packages/2018_Lamnidis_Fennoscandia/2018_Lamnidis_Fennoscandia.ssf diff --git a/packages/2018_Lamnidis_Fennoscandia/2018_Lamnidis_Fennoscandia.ssf b/packages/2018_Lamnidis_Fennoscandia/2018_Lamnidis_Fennoscandia.ssf deleted file mode 100644 index c26ef55..0000000 --- a/packages/2018_Lamnidis_Fennoscandia/2018_Lamnidis_Fennoscandia.ssf +++ /dev/null @@ -1,23 +0,0 @@ -poseidon_IDs udg library_built notes sample_accession study_accession run_accession sample_alias secondary_sample_accession first_public last_updated instrument_model library_layout library_source instrument_platform library_name library_strategy fastq_ftp fastq_aspera fastq_bytes fastq_md5 read_count submitted_ftp -BOO001.A0101 n/a ds n/a SAMEA5043928 PRJEB29360 ERR2857041 BOO001 ERS2855662 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA BOO001.A0101 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2857041/ERR2857041.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/001/ERR2857041/ERR2857041.fastq.gz 172101531 b0dff0511586cd267cb55908d8c4d70c 4997889 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857041/BOO001.A0101.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857041/BOO001.A0101.bam.bai -BOO003.A0101 n/a ds n/a SAMEA5043930 PRJEB29360 ERR2857043 BOO003 ERS2855664 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA BOO003.A0101 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2857043/ERR2857043.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/003/ERR2857043/ERR2857043.fastq.gz 166882210 2bc290ec218aa807285981252a335723 4578933 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857043/BOO003.A0101.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857043/BOO003.A0101.bam.bai -BOO006.A0101 n/a ds n/a SAMEA5043933 PRJEB29360 ERR2857046 BOO006 ERS2855667 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA BOO006.A0101 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2857046/ERR2857046.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/006/ERR2857046/ERR2857046.fastq.gz 159714217 1297d8e5215097d5235c0450c7613057 4376351 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857046/BOO006.A0101.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857046/BOO006.A0101.bam.bai -JK1967 n/a ds n/a SAMEA5043935 PRJEB29360 ERR2857048 JK1967 ERS2855669 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA XXX001.A171061 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2857048/ERR2857048.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/008/ERR2857048/ERR2857048.fastq.gz 3978219 8c56212f7ecab107af29a64eb3515cdc 141089 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857048/JK1967.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857048/JK1967.bam.bai -JK1968 n/a ds n/a SAMEA5043936 PRJEB29360 ERR2857049 JK1968 ERS2855670 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA XXX001.A171062 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2857049/ERR2857049.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/009/ERR2857049/ERR2857049.fastq.gz 84503779 373f663b4e65b97fce3f9b62a45ea2c5 2424594 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857049/JK1968.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857049/JK1968.bam.bai -JK1970 n/a ds n/a SAMEA5043937 PRJEB29360 ERR2857050 JK1970 ERS2855671 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA XXX001.A171063 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2857050/ERR2857050.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/000/ERR2857050/ERR2857050.fastq.gz 59585730 ffa6dc997ba777af49290caf30107929 1804933 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857050/JK1970.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857050/JK1970.bam.bai -JK2067 n/a ds n/a SAMEA5043940 PRJEB29360 ERR2857053 JK2067 ERS2855674 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA XXX001.A171066 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2857053/ERR2857053.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/003/ERR2857053/ERR2857053.fastq.gz 3639370 a0f380b6d9f2f733b4aa73ec0789c91e 125285 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857053/JK2067.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857053/JK2067.bam.bai -JK2065 n/a ds n/a SAMEA5043938 PRJEB29360 ERR2857058 JK2065 ERS2855672 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA XXX001.A16125 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2857058/ERR2857058.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/008/ERR2857058/ERR2857058.fastq.gz 571987279 181b4c3d1de17311ce54aa887b089eb7 16806633 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857058/JK2065.nU.SE.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857058/JK2065.nU.SE.bam.bai -JK1970 n/a ds n/a SAMEA5043937 PRJEB29360 ERR2857060 JK1970 ERS2855671 2018-11-27 2018-11-16 NextSeq 500 SINGLE GENOMIC ILLUMINA XXX001.A16124 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2857060/ERR2857060.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/000/ERR2857060/ERR2857060.fastq.gz 177659257 1057617b149c7b4a568d5508c43f85f8 4547175 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857060/JK1970.nU.PE.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857060/JK1970.nU.PE.bam.bai -JK2065 n/a ds n/a SAMEA5043938 PRJEB29360 ERR2857061 JK2065 ERS2855672 2018-11-27 2018-11-16 NextSeq 500 SINGLE GENOMIC ILLUMINA XXX001.A16125 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2857061/ERR2857061.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/001/ERR2857061/ERR2857061.fastq.gz 155765133 3ad5a9f216fb47fc69db249f5dca1c04 4022905 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857061/JK2065.nU.PE.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857061/JK2065.nU.PE.bam.bai -BOO002.A0101 n/a ds n/a SAMEA5043929 PRJEB29360 ERR2857042 BOO002 ERS2855663 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA BOO002.A0101 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2857042/ERR2857042.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/002/ERR2857042/ERR2857042.fastq.gz 111296254 ecf72befbbab2ba932fff5f2093bdfdf 2798785 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857042/BOO002.A0101.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857042/BOO002.A0101.bam.bai -BOO005.A0101 n/a ds n/a SAMEA5043932 PRJEB29360 ERR2857045 BOO005 ERS2855666 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA BOO005.A0101 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2857045/ERR2857045.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/005/ERR2857045/ERR2857045.fastq.gz 326775388 6ddd68cc153c9580fbb8723531d2ece9 9634975 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857045/BOO005.A0101.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857045/BOO005.A0101.bam.bai -JK2065 n/a ds n/a SAMEA5043938 PRJEB29360 ERR2857051 JK2065 ERS2855672 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA XXX001.A171064 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2857051/ERR2857051.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/001/ERR2857051/ERR2857051.fastq.gz 48338916 1ac63221ff445543cd3a49fa62265231 1524054 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857051/JK2065.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857051/JK2065.bam.bai -JK1970 n/a ds n/a SAMEA5043937 PRJEB29360 ERR2857057 JK1970 ERS2855671 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA XXX001.A16124 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2857057/ERR2857057.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/007/ERR2857057/ERR2857057.fastq.gz 610331876 1f66510c6439b7538dcdf91e9033f111 18080796 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857057/JK1970.nU.SE.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857057/JK1970.nU.SE.bam.bai -BOO004.A0101 n/a ds n/a SAMEA5043931 PRJEB29360 ERR2857044 BOO004 ERS2855665 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA BOO004.A0101 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2857044/ERR2857044.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/004/ERR2857044/ERR2857044.fastq.gz 351467229 74e0b9dd29f31d14f9d5f9f82e083d27 9840133 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857044/BOO004.A0101.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857044/BOO004.A0101.bam.bai -JK1963 n/a ds n/a SAMEA5043934 PRJEB29360 ERR2857047 JK1963 ERS2855668 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA XXX001.A171060 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2857047/ERR2857047.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/007/ERR2857047/ERR2857047.fastq.gz 5449546 ad8e4cfadde42dc2563e7e2f2764e995 173258 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857047/JK1963.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857047/JK1963.bam.bai -JK2066 n/a ds n/a SAMEA5043939 PRJEB29360 ERR2857052 JK2066 ERS2855673 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA XXX001.A171065 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2857052/ERR2857052.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/002/ERR2857052/ERR2857052.fastq.gz 4498748 14007200e4b6b65513fb73dc60206ebd 159257 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857052/JK2066.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857052/JK2066.bam.bai -CHV001.A0101 n/a ds n/a SAMEA5043941 PRJEB29360 ERR2857054 CHV001 ERS2855675 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA CHV001.A0101 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2857054/ERR2857054.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/004/ERR2857054/ERR2857054.fastq.gz 177880280 7c167608f9d493a29f7584b6a7fdff0f 4940474 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857054/CHV001.A0101.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857054/CHV001.A0101.bam.bai -CHV002.A0101 n/a ds n/a SAMEA5043942 PRJEB29360 ERR2857055 CHV002 ERS2855676 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA CHV002.A0101 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2857055/ERR2857055.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/005/ERR2857055/ERR2857055.fastq.gz 106341886 dc4e782cc8e071c7c70e2c7113cf74b0 2820563 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857055/CHV002.A0101.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857055/CHV002.A0101.bam.bai -JK1968 n/a ds n/a SAMEA5043936 PRJEB29360 ERR2857056 JK1968 ERS2855670 2018-11-27 2018-11-16 Illumina HiSeq 4000 SINGLE GENOMIC ILLUMINA XXX001.A16123 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2857056/ERR2857056.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/006/ERR2857056/ERR2857056.fastq.gz 494908398 bbfd94a8fe91e4d6c2dfa9caf8324f79 15193613 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857056/JK1968.nU.SE.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857056/JK1968.nU.SE.bam.bai -JK1968 n/a ds n/a SAMEA5043936 PRJEB29360 ERR2857059 JK1968 ERS2855670 2018-11-27 2018-11-16 NextSeq 500 SINGLE GENOMIC ILLUMINA XXX001.A16123 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2857059/ERR2857059.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/009/ERR2857059/ERR2857059.fastq.gz 169406455 6f4ff1b7097e863adb71b0c6b5f92ab7 4454175 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857059/JK1968.nU.PE.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857059/JK1968.nU.PE.bam.bai -Saami001 plus n/a Present-day data, so no damage. Set udg to 'plus' SAMEA5043943 PRJEB29360 ERR2857062 Saami001 ERS2855677 2018-11-27 2018-11-16 Illumina Genome Analyzer II PAIRED GENOMIC ILLUMINA Saami_090511 WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2857062/ERR2857062.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2857062/ERR2857062_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2857062/ERR2857062_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/002/ERR2857062/ERR2857062.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/002/ERR2857062/ERR2857062_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR285/002/ERR2857062/ERR2857062_2.fastq.gz 341167554;25011768303;25286553258 3ba1e49107855df725523c4d84757c0f;230cf4747534e9d154b2a9801aa6a51b;3a1be192a3a8d7655cd4b291c5da65d5 233869444 ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857062/Saami.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2857062/Saami.bam.bai From cb875cbfb3d7bbe2488cbf5e31e53328e10a8bea Mon Sep 17 00:00:00 2001 From: Thiseas Christos Lamnidis Date: Thu, 18 Jul 2024 11:44:07 +0200 Subject: [PATCH 03/12] Add SSF for 2023_Salazar_MachuPicchu --- .../2023_Salazar_MachuPicchu.ssf | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.ssf diff --git a/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.ssf b/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.ssf new file mode 100644 index 0000000..02ababd --- /dev/null +++ b/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.ssf @@ -0,0 +1,57 @@ +poseidon_IDs udg library_built notes sample_accession study_accession run_accession sample_alias secondary_sample_accession first_public last_updated instrument_model library_layout library_source instrument_platform library_name library_strategy fastq_ftp fastq_aspera fastq_bytes fastq_md5 read_count submitted_ftp +KCA-3089 half ds n/a SAMEA113570544 PRJEB62808 ERR11518429 KCA-3089 ERS15565536 2023-07-19 2023-07-19 NextSeq 500 SINGLE GENOMIC ILLUMINA KCA-3089 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/029/ERR11518429/ERR11518429.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/029/ERR11518429/ERR11518429.fastq.gz 258055876 046ce720f99c9c0e156de88745b24daf 6693369 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518429/KCA-3089.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518429/KCA-3089.clip.s.f.rg.bam.bai +KCA-1108 half ds n/a SAMEA113570541 PRJEB62808 ERR11518434 KCA-1108 ERS15565533 2023-07-19 2023-07-19 NextSeq 500 SINGLE GENOMIC ILLUMINA KCA-1108 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/034/ERR11518434/ERR11518434.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/034/ERR11518434/ERR11518434.fastq.gz 340722485 411f907d8f9b3046bb076446fdd1a91f 10338752 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518434/KCA-1108.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518434/KCA-1108.clip.s.f.rg.bam.bai +KCA-1364 half ds n/a SAMEA113570543 PRJEB62808 ERR11518435 KCA-1364 ERS15565535 2023-07-19 2023-07-19 NextSeq 500 SINGLE GENOMIC ILLUMINA KCA-1364 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/035/ERR11518435/ERR11518435.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/035/ERR11518435/ERR11518435.fastq.gz 351929329 22cda8a00f616941c867a549d5998013 10143884 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518435/KCA-1364.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518435/KCA-1364.clip.s.f.rg.bam.bai +MP13 half ds n/a SAMEA113570550 PRJEB62808 ERR11518444 MP13 ERS15565542 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP13 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/044/ERR11518444/ERR11518444.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/044/ERR11518444/ERR11518444_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/044/ERR11518444/ERR11518444_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/044/ERR11518444/ERR11518444.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/044/ERR11518444/ERR11518444_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/044/ERR11518444/ERR11518444_2.fastq.gz 1368656;49028;50644 e9ef0c546b1da0ec8bd0cf4c7d10cae9;62dc0f8e8f5b1ab6656b977784befbab;62a0e55047036cceb1b47154fe2c4a9a 51217 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518444/MP13.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518444/MP13.clip.s.f.rg.bam.bai +KMA-28-1 half ds n/a SAMEA113570548 PRJEB62808 ERR11518463 KMA-28-1 ERS15565540 2023-07-19 2023-07-19 NextSeq 500 SINGLE GENOMIC ILLUMINA KMA-28-1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/063/ERR11518463/ERR11518463.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/063/ERR11518463/ERR11518463.fastq.gz 483345805 e1bdba5a68dec9dd3e0e419a25fbde61 12834649 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518463/KMA-28-1.clip.s.f.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518463/KMA-28-1.clip.s.f.bam.bai +MP33 half ds n/a SAMEA113570555 PRJEB62808 ERR11518465 MP33 ERS15565547 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP33 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/065/ERR11518465/ERR11518465.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/065/ERR11518465/ERR11518465_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/065/ERR11518465/ERR11518465_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/065/ERR11518465/ERR11518465.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/065/ERR11518465/ERR11518465_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/065/ERR11518465/ERR11518465_2.fastq.gz 29860878;2234387;2396086 f1a7a08be610136fae4986e12ce9f15f;0a33ac86fc0c8610925942f078b5cbc4;198cd90ec1363b3056d6d0ecd5bb0c01 1023906 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518465/MP33.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518465/MP33.clip.s.f.rg.bam.bai +MP42B half ds n/a SAMEA113570558 PRJEB62808 ERR11518471 MP42B ERS15565550 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP42B Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/071/ERR11518471/ERR11518471.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/071/ERR11518471/ERR11518471_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/071/ERR11518471/ERR11518471_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/071/ERR11518471/ERR11518471.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/071/ERR11518471/ERR11518471_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/071/ERR11518471/ERR11518471_2.fastq.gz 35926892;3228124;3428986 bcea899b4c50a710b5c3b5a9d8e51512;543c9878ac77e20b1ba652509e1f6fe6;792a86eaaab3e8d1130af7a9a664add0 1275363 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518471/MP42B.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518471/MP42B.clip.s.f.rg.bam.bai +MP42A half ds n/a SAMEA113570557 PRJEB62808 ERR11518472 MP42A ERS15565549 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP42A Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/072/ERR11518472/ERR11518472.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/072/ERR11518472/ERR11518472_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/072/ERR11518472/ERR11518472_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/072/ERR11518472/ERR11518472.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/072/ERR11518472/ERR11518472_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/072/ERR11518472/ERR11518472_2.fastq.gz 43044181;1705607;1772582 4ec13677227a6dfc84251ed996f0ac95;658eac60413be1d0f08047a080af3b28;b09465fb2911e1b6b44e596de6a4cf3e 1462380 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518472/MP42A.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518472/MP42A.clip.s.f.rg.bam.bai +MP48B half ds n/a SAMEA113570561 PRJEB62808 ERR11518477 MP48B ERS15565553 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP48B Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/077/ERR11518477/ERR11518477.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/077/ERR11518477/ERR11518477_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/077/ERR11518477/ERR11518477_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/077/ERR11518477/ERR11518477.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/077/ERR11518477/ERR11518477_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/077/ERR11518477/ERR11518477_2.fastq.gz 34151303;4551952;4743311 f20b90909e361c7133e1d2abb7f92918;0312de63f1fa778e9ad9b245765b6631;d71d59e142a135321784b158d802c64c 1278229 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518477/MP48B.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518477/MP48B.clip.s.f.rg.bam.bai +MP50A half ds n/a SAMEA113570567 PRJEB62808 ERR11518484 MP50A ERS15565559 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP50A Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/084/ERR11518484/ERR11518484.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/084/ERR11518484/ERR11518484_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/084/ERR11518484/ERR11518484_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/084/ERR11518484/ERR11518484.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/084/ERR11518484/ERR11518484_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/084/ERR11518484/ERR11518484_2.fastq.gz 14099112;966482;1012658 51d281225ba141012e04609b0ce94c3e;c7f58b994322b8e7aae03d4905779515;9c13ab6e80656afc0a42ea15f2146ae3 487566 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518484/MP50A.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518484/MP50A.clip.s.f.rg.bam.bai +MP4f half ds n/a SAMEA113570565 PRJEB62808 ERR11518485 MP4f ERS15565557 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP4f Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/085/ERR11518485/ERR11518485.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/085/ERR11518485/ERR11518485_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/085/ERR11518485/ERR11518485_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/085/ERR11518485/ERR11518485.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/085/ERR11518485/ERR11518485_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/085/ERR11518485/ERR11518485_2.fastq.gz 44016477;322399;326222 94b89a8ce8e213cd90d0e5cc20f12fdf;9c9be9adb3dacf8a7bb690d2f78c938e;cc2f090e9742ffb046739ec2550c679e 1404851 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518485/MP4f.s.f.MD.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518485/MP4f.s.f.MD.bam.bai +MP4i half ds n/a SAMEA113570566 PRJEB62808 ERR11518489 MP4i ERS15565558 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP4i Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/089/ERR11518489/ERR11518489.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/089/ERR11518489/ERR11518489_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/089/ERR11518489/ERR11518489_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/089/ERR11518489/ERR11518489.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/089/ERR11518489/ERR11518489_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/089/ERR11518489/ERR11518489_2.fastq.gz 60506515;6138768;6466047 d9985f02a0135bb2412a9ef26d07a9b3;43db5492532d81bd248e333b65267368;966cf942e081be98e835d70bc728eb91 2180758 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518489/MP4i.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518489/MP4i.clip.s.f.rg.bam.bai +MP5A half ds n/a SAMEA113570571 PRJEB62808 ERR11518495 MP5A ERS15565563 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP5A Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/095/ERR11518495/ERR11518495.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/095/ERR11518495/ERR11518495_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/095/ERR11518495/ERR11518495_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/095/ERR11518495/ERR11518495.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/095/ERR11518495/ERR11518495_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/095/ERR11518495/ERR11518495_2.fastq.gz 93507551;14275665;15148221 ddd1ba9dcaf624e5d91afa0b8dc3b37e;71fa999845cf54406ee9f6ed022c9e02;d7d8065a9e7bdfcebd2058a12f11be77 3635500 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518495/MP5A.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518495/MP5A.clip.s.f.rg.bam.bai +MP65B half ds n/a SAMEA113570574 PRJEB62808 ERR11518496 MP65B ERS15565566 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP65B Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/096/ERR11518496/ERR11518496.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/096/ERR11518496/ERR11518496_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/096/ERR11518496/ERR11518496_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/096/ERR11518496/ERR11518496.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/096/ERR11518496/ERR11518496_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/096/ERR11518496/ERR11518496_2.fastq.gz 1685557;54800;57296 d308cddfae83f3acd71d936c397e21c7;79e467fea7fd5f343bd1391d54272027;d4f3cc5c579250e8dff1fac3924ef077 54929 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518496/MP65B.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518496/MP65B.clip.s.f.rg.bam.bai +MP27 half ds n/a SAMEA113570552 PRJEB62808 ERR11518499 MP27 ERS15565544 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP27 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/099/ERR11518499/ERR11518499.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/099/ERR11518499/ERR11518499_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/099/ERR11518499/ERR11518499_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/099/ERR11518499/ERR11518499.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/099/ERR11518499/ERR11518499_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/099/ERR11518499/ERR11518499_2.fastq.gz 601202918;6230169;6565406 2ea0372069328031e0fe3db3ab9823e8;239edaf52749c7bb2750dfccf65973fa;5026a3a920ec334007c0c5aabececb9f 16435400 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518499/MP27.clip.s.f.MD.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518499/MP27.clip.s.f.MD.rg.bam.bai +OTT-1144 half ds n/a SAMEA113570583 PRJEB62808 ERR11518523 OTT-1144 ERS15565575 2023-07-19 2023-07-19 NextSeq 500 SINGLE GENOMIC ILLUMINA OTT-1144 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/023/ERR11518523/ERR11518523.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/023/ERR11518523/ERR11518523.fastq.gz 251719724 9a3f492385b17bc8bd5b75ac6384276b 6511305 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518523/OTT-1144.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518523/OTT-1144.clip.s.f.rg.bam.bai +MP61 half ds n/a SAMEA113570572 PRJEB62808 ERR11518546 MP61 ERS15565564 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP61 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/046/ERR11518546/ERR11518546.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/046/ERR11518546/ERR11518546_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/046/ERR11518546/ERR11518546_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/046/ERR11518546/ERR11518546.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/046/ERR11518546/ERR11518546_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/046/ERR11518546/ERR11518546_2.fastq.gz 1067460047;1490709;1604171 e43be0ce26cc3e2a70e74398aaa295b6;79f8dfe08a484a9441aefbcda2f7e191;66b35652e35c17843d83635c8a1b4c8c 30831057 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518546/MP61.clip.s.f.MD.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518546/MP61.clip.s.f.MD.rg.bam.bai +QKI-21-1 half ds n/a SAMEA113570588 PRJEB62808 ERR11518553 QKI-21-1 ERS15565580 2023-07-19 2023-07-19 NextSeq 500 SINGLE GENOMIC ILLUMINA QKI-21-1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/053/ERR11518553/ERR11518553.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/053/ERR11518553/ERR11518553.fastq.gz 40394192 0be1343ce2412dab6f068db37e7b9906 1261280 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518553/QKI-21-1.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518553/QKI-21-1.clip.s.f.rg.bam.bai +MP31A half ds n/a SAMEA113570553 PRJEB62808 ERR11518458 MP31A ERS15565545 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP31A Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/058/ERR11518458/ERR11518458.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/058/ERR11518458/ERR11518458_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/058/ERR11518458/ERR11518458_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/058/ERR11518458/ERR11518458.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/058/ERR11518458/ERR11518458_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/058/ERR11518458/ERR11518458_2.fastq.gz 27445334;2911041;3065223 4c25535bcad27dfd124862e01f08224b;c0983f0e8cf9b4aa7fdcdfabee23824f;91c5d561d67b651a47a95bc8db813b10 1013759 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518458/MP31A.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518458/MP31A.clip.s.f.rg.bam.bai +KMA-15A-1 half ds n/a SAMEA113570545 PRJEB62808 ERR11518461 KMA-15A-1 ERS15565537 2023-07-19 2023-07-19 NextSeq 500 SINGLE GENOMIC ILLUMINA KMA-15A-1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/061/ERR11518461/ERR11518461.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/061/ERR11518461/ERR11518461.fastq.gz 556397705 922d79be1a86e955552b07e3f20bb2b2 15468537 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518461/KMA-15A-1.clip.s.f.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518461/KMA-15A-1.clip.s.f.bam.bai +MP45A half ds n/a SAMEA113570560 PRJEB62808 ERR11518475 MP45A ERS15565552 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP45A Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/075/ERR11518475/ERR11518475.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/075/ERR11518475/ERR11518475_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/075/ERR11518475/ERR11518475_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/075/ERR11518475/ERR11518475.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/075/ERR11518475/ERR11518475_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/075/ERR11518475/ERR11518475_2.fastq.gz 49839111;7776441;7679233 3d257ef3c54b960643e2b188a8c5cc98;77c4f9f922529294d69e236338cd30dc;d39a08d09c7ae2033661518a80e85a85 1850331 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518475/MP45A.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518475/MP45A.clip.s.f.rg.bam.bai +MP4E half ds n/a SAMEA113570564 PRJEB62808 ERR11518480 MP4E ERS15565556 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP4E Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/080/ERR11518480/ERR11518480.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/080/ERR11518480/ERR11518480_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/080/ERR11518480/ERR11518480_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/080/ERR11518480/ERR11518480.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/080/ERR11518480/ERR11518480_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/080/ERR11518480/ERR11518480_2.fastq.gz 14044404;963775;1006539 f7911f4b3861a0bea82e34438f959fe8;fcdeea9cf0a63c70877d8cb1a02d5470;eb82fd238f227606e6cc825398c254ac 487170 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518480/MP4E.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518480/MP4E.clip.s.f.rg.bam.bai +MP4D half ds n/a SAMEA113570563 PRJEB62808 ERR11518481 MP4D ERS15565555 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP4D Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/081/ERR11518481/ERR11518481.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/081/ERR11518481/ERR11518481_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/081/ERR11518481/ERR11518481_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/081/ERR11518481/ERR11518481.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/081/ERR11518481/ERR11518481_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/081/ERR11518481/ERR11518481_2.fastq.gz 23219574;2197257;2284521 f17e88dbea4b5885523a5bd7d55e6fd1;3792b331daa882de0cfabc62ff82c9ff;96f4f6b10fc9b18cfaceca6538d8c4b4 822592 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518481/MP4D.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518481/MP4D.clip.s.f.rg.bam.bai +MP53A half ds n/a SAMEA113570569 PRJEB62808 ERR11518486 MP53A ERS15565561 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP53A Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/086/ERR11518486/ERR11518486.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/086/ERR11518486/ERR11518486_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/086/ERR11518486/ERR11518486_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/086/ERR11518486/ERR11518486.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/086/ERR11518486/ERR11518486_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/086/ERR11518486/ERR11518486_2.fastq.gz 5133756;353536;371190 36724522fe9f8fd20e9d5bcd4819bbc2;778f83b282547bd214481321a4dd9d7a;a5ead58691534f3727aafc6b95339d51 179453 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518486/MP53A.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518486/MP53A.clip.s.f.rg.bam.bai +MP55 half ds n/a SAMEA113570570 PRJEB62808 ERR11518487 MP55 ERS15565562 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP55 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/087/ERR11518487/ERR11518487.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/087/ERR11518487/ERR11518487_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/087/ERR11518487/ERR11518487_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/087/ERR11518487/ERR11518487.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/087/ERR11518487/ERR11518487_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/087/ERR11518487/ERR11518487_2.fastq.gz 6534957;302090;332138 5bc19982d7bf9743dd09004a11e21e34;c59c3f8935f330661af52bdb2e8f8173;6ee2fd449ab2bfae0ec97e0d23f5ad89 216693 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518487/MP55.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518487/MP55.clip.s.f.rg.bam.bai +MP78A half ds n/a SAMEA113570577 PRJEB62808 ERR11518501 MP78A ERS15565569 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP78A Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/001/ERR11518501/ERR11518501.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/001/ERR11518501/ERR11518501_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/001/ERR11518501/ERR11518501_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/001/ERR11518501/ERR11518501.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/001/ERR11518501/ERR11518501_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/001/ERR11518501/ERR11518501_2.fastq.gz 10594823;768121;809123 2a930d3feffe2da654007b3b5205c847;adcba2f6ab14eb007840ef3bfcd8ccc5;0d9da102f7c71b0a2a32a0a62ecb29d1 374555 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518501/MP78A.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518501/MP78A.clip.s.f.rg.bam.bai +MP84A half ds n/a SAMEA113570580 PRJEB62808 ERR11518514 MP84A ERS15565572 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP84A Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/014/ERR11518514/ERR11518514.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/014/ERR11518514/ERR11518514_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/014/ERR11518514/ERR11518514_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/014/ERR11518514/ERR11518514.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/014/ERR11518514/ERR11518514_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/014/ERR11518514/ERR11518514_2.fastq.gz 33851298;3245477;3388441 7bfe165c0596dcd12ec96d1a8325527d;ddad64e98c12d38a3f52e09dc2f438e4;f5c1732d314667e8b65533de766c4044 1215070 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518514/MP84A.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518514/MP84A.clip.s.f.rg.bam.bai +QKI-809 half ds n/a SAMEA113570590 PRJEB62808 ERR11518566 QKI-809 ERS15565582 2023-07-19 2023-07-19 NextSeq 500 SINGLE GENOMIC ILLUMINA QKI-809 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/066/ERR11518566/ERR11518566.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/066/ERR11518566/ERR11518566.fastq.gz 280526353 6c62e3a05f281e9e88fe3d8a56174f2e 7530496 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518566/QKI-809.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518566/QKI-809.clip.s.f.rg.bam.bai +QKI-9-3 half ds n/a SAMEA113570591 PRJEB62808 ERR11518572 QKI-9-3 ERS15565583 2023-07-19 2023-07-19 NextSeq 500 SINGLE GENOMIC ILLUMINA QKI-9-3 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/072/ERR11518572/ERR11518572.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/072/ERR11518572/ERR11518572.fastq.gz 125805571 c934e3e9a519ad8b53194a2c3fb7ed29 3667870 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518572/QKI-9-3.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518572/QKI-9-3.clip.s.f.rg.bam.bai +SHN-575 half ds n/a SAMEA113570595 PRJEB62808 ERR11518597 SHN-575 ERS15565587 2023-07-19 2023-07-19 NextSeq 500 SINGLE GENOMIC ILLUMINA SHN-575 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/097/ERR11518597/ERR11518597.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/097/ERR11518597/ERR11518597.fastq.gz 427909329 2d9ede8c7decbf95ece2c66142f381e1 13050061 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518597/SHN-575.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518597/SHN-575.clip.s.f.rg.bam.bai +KCA-1298 half ds n/a SAMEA113570542 PRJEB62808 ERR11518432 KCA-1298 ERS15565534 2023-07-19 2023-07-19 NextSeq 500 SINGLE GENOMIC ILLUMINA KCA-1298 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/032/ERR11518432/ERR11518432.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/032/ERR11518432/ERR11518432.fastq.gz 320940192 5cbd1960b7facfb8f6cf9a357511edfb 9736465 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518432/KCA-1298.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518432/KCA-1298.clip.s.f.rg.bam.bai +CCA-7-2 half ds n/a SAMEA113570540 PRJEB62808 ERR11518440 CCA-7-2 ERS15565532 2023-07-19 2023-07-19 NextSeq 500 SINGLE GENOMIC ILLUMINA CCA-7-2 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/040/ERR11518440/ERR11518440.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/040/ERR11518440/ERR11518440.fastq.gz 476983394 547f8469950d5fc088f9f4e9470ac1f8 13487974 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518440/CCA-7-2.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518440/CCA-7-2.clip.s.f.rg.bam.bai +MP107B half ds n/a SAMEA113570549 PRJEB62808 ERR11518443 MP107B ERS15565541 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP107B Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/043/ERR11518443/ERR11518443.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/043/ERR11518443/ERR11518443_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/043/ERR11518443/ERR11518443_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/043/ERR11518443/ERR11518443.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/043/ERR11518443/ERR11518443_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/043/ERR11518443/ERR11518443_2.fastq.gz 20472796;1714736;1808590 df6dc5bc4a9aecdbc02068cb49138f63;bdb74f9565e812047aac47689c9bfe57;c4e726c1c6829b74be7db132f657fc25 712461 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518443/MP107B.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518443/MP107B.clip.s.f.rg.bam.bai +MP23 half ds n/a SAMEA113570551 PRJEB62808 ERR11518448 MP23 ERS15565543 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP23 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/048/ERR11518448/ERR11518448.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/048/ERR11518448/ERR11518448_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/048/ERR11518448/ERR11518448_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/048/ERR11518448/ERR11518448.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/048/ERR11518448/ERR11518448_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/048/ERR11518448/ERR11518448_2.fastq.gz 50991672;6126164;6440129 ddc85aceace7906cd0158ed7c71ab737;1a306cc24ad62c33d87de5a350891e3a;ec5c0d3a87ec94c2016d53d222a1e4ba 1894425 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518448/MP23.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518448/MP23.clip.s.f.rg.bam.bai +KMA-2-2 half ds n/a SAMEA113570547 PRJEB62808 ERR11518456 KMA-2-2 ERS15565539 2023-07-19 2023-07-19 NextSeq 500 SINGLE GENOMIC ILLUMINA KMA-2-2 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/056/ERR11518456/ERR11518456.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/056/ERR11518456/ERR11518456.fastq.gz 372015877 0d6dd2a57f5bcfdb28735bd438c82a79 9949155 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518456/KMA-2-2.clip.s.f.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518456/KMA-2-2.clip.s.f.bam.bai +MP32 half ds n/a SAMEA113570554 PRJEB62808 ERR11518466 MP32 ERS15565546 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP32 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/066/ERR11518466/ERR11518466.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/066/ERR11518466/ERR11518466_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/066/ERR11518466/ERR11518466_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/066/ERR11518466/ERR11518466.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/066/ERR11518466/ERR11518466_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/066/ERR11518466/ERR11518466_2.fastq.gz 65706996;7118517;7473311 cbbeab1efd2c8eeb619c7d915ca1ddc0;578cd6786e6241366ba1cf491967759a;f6da2296e7d3ac4a3926d5c7562db054 2413528 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518466/MP32.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518466/MP32.clip.s.f.rg.bam.bai +KMA-19-1 half ds n/a SAMEA113570546 PRJEB62808 ERR11518467 KMA-19-1 ERS15565538 2023-07-19 2023-07-19 NextSeq 500 SINGLE GENOMIC ILLUMINA KMA-19-1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/067/ERR11518467/ERR11518467.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/067/ERR11518467/ERR11518467.fastq.gz 523024651 05a0c1c8be8277eee4fa833298396f66 15197325 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518467/KMA-19-1.clip.s.f.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518467/KMA-19-1.clip.s.f.bam.bai +MP42C half ds n/a SAMEA113570559 PRJEB62808 ERR11518469 MP42C ERS15565551 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP42C Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/069/ERR11518469/ERR11518469.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/069/ERR11518469/ERR11518469_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/069/ERR11518469/ERR11518469_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/069/ERR11518469/ERR11518469.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/069/ERR11518469/ERR11518469_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/069/ERR11518469/ERR11518469_2.fastq.gz 5403837;293785;309110 3e36d90fdcb5f351f53ae225380eb4a7;40941c2535998302b334fdecf49f357f;5a55558d80313a286758ddc325d29e7d 193132 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518469/MP42C.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518469/MP42C.clip.s.f.rg.bam.bai +MP4B half ds n/a SAMEA113570562 PRJEB62808 ERR11518478 MP4B ERS15565554 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP4B Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/078/ERR11518478/ERR11518478.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/078/ERR11518478/ERR11518478_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/078/ERR11518478/ERR11518478_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/078/ERR11518478/ERR11518478.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/078/ERR11518478/ERR11518478_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/078/ERR11518478/ERR11518478_2.fastq.gz 48671068;3269399;3402506 66f76c64a192c3bfb544965c758397a7;cac225da272fde6ce2813e70a5730ddb;87a50ba638ab557771aab278180c11a4 1669200 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518478/MP4B.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518478/MP4B.clip.s.f.rg.bam.bai +MP51 half ds n/a SAMEA113570568 PRJEB62808 ERR11518493 MP51 ERS15565560 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP51 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/093/ERR11518493/ERR11518493.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/093/ERR11518493/ERR11518493_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/093/ERR11518493/ERR11518493_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/093/ERR11518493/ERR11518493.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/093/ERR11518493/ERR11518493_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/093/ERR11518493/ERR11518493_2.fastq.gz 126035457;9735721;10188812 f05397f1f5e3a3f91f3fb0dc645dff1a;1700c57f67573ba98c21127ae8075f1c;35dffe6cc3af13bb5520396316d7b678 4449703 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518493/MP51.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518493/MP51.clip.s.f.rg.bam.bai +MP71 half ds n/a SAMEA113570575 PRJEB62808 ERR11518498 MP71 ERS15565567 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP71 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/098/ERR11518498/ERR11518498.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/098/ERR11518498/ERR11518498_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/098/ERR11518498/ERR11518498_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/098/ERR11518498/ERR11518498.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/098/ERR11518498/ERR11518498_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/098/ERR11518498/ERR11518498_2.fastq.gz 24950336;1919625;2093061 52272412d23a124bba52d1c931443948;e31605af48be3c881a34df042da9d188;f8ab4bdf361e0d9926bd4ef3b2efb90c 846267 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518498/MP71.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518498/MP71.clip.s.f.rg.bam.bai +MP77A half ds n/a SAMEA113570576 PRJEB62808 ERR11518500 MP77A ERS15565568 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP77A Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/000/ERR11518500/ERR11518500.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/000/ERR11518500/ERR11518500_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/000/ERR11518500/ERR11518500_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/000/ERR11518500/ERR11518500.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/000/ERR11518500/ERR11518500_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/000/ERR11518500/ERR11518500_2.fastq.gz 21841982;1063929;1098970 afc180a2dcc04775de12d2f552b3604b;88041f8ee8afdfa90468c073f1e6431f;eb22934ecdf6fcb0d178d373dd9528b1 746501 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518500/MP77A.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518500/MP77A.clip.s.f.rg.bam.bai +MP82 half ds n/a SAMEA113570579 PRJEB62808 ERR11518502 MP82 ERS15565571 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP82 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/002/ERR11518502/ERR11518502.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/002/ERR11518502/ERR11518502_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/002/ERR11518502/ERR11518502_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/002/ERR11518502/ERR11518502.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/002/ERR11518502/ERR11518502_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/002/ERR11518502/ERR11518502_2.fastq.gz 1212666;50309;52852 5e472474b34c41828c55d18f3ac0c124;f2d7363a789c338ccf5af14a41a8f0fe;7d4d5ea62b7f5ccd004d52bab9acd11e 42163 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518502/MP82.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518502/MP82.clip.s.f.rg.bam.bai +MP80 half ds n/a SAMEA113570578 PRJEB62808 ERR11518503 MP80 ERS15565570 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP80 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/003/ERR11518503/ERR11518503.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/003/ERR11518503/ERR11518503_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/003/ERR11518503/ERR11518503_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/003/ERR11518503/ERR11518503.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/003/ERR11518503/ERR11518503_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/003/ERR11518503/ERR11518503_2.fastq.gz 6349908;314718;332287 10fd16b3f457fe96b83f87536b027b0b;354a7e15fe3d9fe31a71f97b2dd63464;57c5dfbf3abc6eaa336b0142ae329cd1 220724 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518503/MP80.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518503/MP80.clip.s.f.rg.bam.bai +MP84C half ds n/a SAMEA113570581 PRJEB62808 ERR11518512 MP84C ERS15565573 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP84C Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/012/ERR11518512/ERR11518512.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/012/ERR11518512/ERR11518512_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/012/ERR11518512/ERR11518512_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/012/ERR11518512/ERR11518512.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/012/ERR11518512/ERR11518512_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/012/ERR11518512/ERR11518512_2.fastq.gz 23961145;1088516;1139989 57ec431d7936df1c2707ffa1ab304dfd;8884b15583c3b5a766b1c77d030dcb33;eace0ad23d367e13660bb06befc1505b 813558 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518512/MP84C.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518512/MP84C.clip.s.f.rg.bam.bai +OTT-1160 half ds n/a SAMEA113570584 PRJEB62808 ERR11518538 OTT-1160 ERS15565576 2023-07-19 2023-07-19 NextSeq 500 SINGLE GENOMIC ILLUMINA OTT-1160 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/038/ERR11518538/ERR11518538.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/038/ERR11518538/ERR11518538.fastq.gz 391401875 dc3104ef5c203d7010095690e8bd4f3c 11078709 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518538/OTT-1160.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518538/OTT-1160.clip.s.f.rg.bam.bai +OTT-1165 half ds n/a SAMEA113570585 PRJEB62808 ERR11518543 OTT-1165 ERS15565577 2023-07-19 2023-07-19 NextSeq 500 SINGLE GENOMIC ILLUMINA OTT-1165 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/043/ERR11518543/ERR11518543.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/043/ERR11518543/ERR11518543.fastq.gz 127065502 09d809235bb8386a7715d8d54aa215f0 3505275 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518543/OTT-1165.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518543/OTT-1165.clip.s.f.rg.bam.bai +MP63 half ds n/a SAMEA113570573 PRJEB62808 ERR11518550 MP63 ERS15565565 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP63 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/050/ERR11518550/ERR11518550.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/050/ERR11518550/ERR11518550_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/050/ERR11518550/ERR11518550_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/050/ERR11518550/ERR11518550.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/050/ERR11518550/ERR11518550_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/050/ERR11518550/ERR11518550_2.fastq.gz 973779168;19974143;20873641 b0cceeafc96cba47cfac6534f6d6ae9e;d131eff535623ec8812fc6b5fb3066ce;27e3e56cd0cd0749d167cc6002da5276 28542497 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518550/MP63.clip.s.f.MD.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518550/MP63.clip.s.f.MD.rg.bam.bai +OTT-1174 half ds n/a SAMEA113570586 PRJEB62808 ERR11518552 OTT-1174 ERS15565578 2023-07-19 2023-07-19 NextSeq 500 SINGLE GENOMIC ILLUMINA OTT-1174 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/052/ERR11518552/ERR11518552.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/052/ERR11518552/ERR11518552.fastq.gz 157547868 5d53c3a01dbacc65dbdce5a8b39ab656 4336131 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518552/OTT-1174.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518552/OTT-1174.clip.s.f.rg.bam.bai +QKI-4 half ds n/a SAMEA113570589 PRJEB62808 ERR11518562 QKI-4 ERS15565581 2023-07-19 2023-07-19 NextSeq 500 SINGLE GENOMIC ILLUMINA QKI-4 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/062/ERR11518562/ERR11518562.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/062/ERR11518562/ERR11518562.fastq.gz 215455792 249f0108a09a0b3562e15deda514255d 6284579 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518562/QKI-4.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518562/QKI-4.clip.s.f.rg.bam.bai +OTT-1187 half ds n/a SAMEA113570587 PRJEB62808 ERR11518565 OTT-1187 ERS15565579 2023-07-19 2023-07-19 NextSeq 500 SINGLE GENOMIC ILLUMINA OTT-1187 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/065/ERR11518565/ERR11518565.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/065/ERR11518565/ERR11518565.fastq.gz 395522079 3f0dbf88b811adc59f4a3a949f95b3b9 10883525 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518565/OTT-1187.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518565/OTT-1187.clip.s.f.rg.bam.bai +SHN-212 half ds n/a SAMEA113570592 PRJEB62808 ERR11518568 SHN-212 ERS15565584 2023-07-19 2023-07-19 NextSeq 500 SINGLE GENOMIC ILLUMINA SHN-212 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/068/ERR11518568/ERR11518568.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/068/ERR11518568/ERR11518568.fastq.gz 34758038 bb0e7bc6a37461d2891a0c7e71204a79 1222346 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518568/SHN-212.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518568/SHN-212.clip.s.f.rg.bam.bai +SHN-355 half ds n/a SAMEA113570593 PRJEB62808 ERR11518578 SHN-355 ERS15565585 2023-07-19 2023-07-19 NextSeq 500 SINGLE GENOMIC ILLUMINA SHN-355 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/078/ERR11518578/ERR11518578.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/078/ERR11518578/ERR11518578.fastq.gz 190960107 c8471b944f9529bc482c4d56237dabed 5226978 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518578/SHN-355.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518578/SHN-355.clip.s.f.rg.bam.bai +SHN-492 half ds n/a SAMEA113570594 PRJEB62808 ERR11518582 SHN-492 ERS15565586 2023-07-19 2023-07-19 NextSeq 500 SINGLE GENOMIC ILLUMINA SHN-492 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/082/ERR11518582/ERR11518582.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/082/ERR11518582/ERR11518582.fastq.gz 211215016 7508d5373da6bdf2ba60c3c9359d7eef 5775705 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518582/SHN-492.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518582/SHN-492.clip.s.f.rg.bam.bai +SHN-902 half ds n/a SAMEA113570596 PRJEB62808 ERR11518584 SHN-902 ERS15565588 2023-07-19 2023-07-19 NextSeq 500 SINGLE GENOMIC ILLUMINA SHN-902 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/084/ERR11518584/ERR11518584.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/084/ERR11518584/ERR11518584.fastq.gz 61258729 fbd3b91ca910e0057595aeb33333af8a 1862554 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518584/SHN-902.clip.s.f.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518584/SHN-902.clip.s.f.rg.bam.bai +MP3a half ds n/a SAMEA113570556 PRJEB62808 ERR11518632 MP3a ERS15565548 2023-07-19 2023-07-19 NextSeq 500 PAIRED GENOMIC ILLUMINA MP3a Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/032/ERR11518632/ERR11518632.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/032/ERR11518632/ERR11518632_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR115/032/ERR11518632/ERR11518632_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/032/ERR11518632/ERR11518632.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/032/ERR11518632/ERR11518632_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR115/032/ERR11518632/ERR11518632_2.fastq.gz 1084204480;14624478;15625220 1b3a472e7e915626c4f23bde4193f7ab;d64857a70d380688f0d96c7e39b4bf46;b433d42c36a1d55666606cf266802fad 31614652 ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518632/MP3a.clip.s.f.MD.rg.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR115/ERR11518632/MP3a.clip.s.f.MD.rg.bam.bai From 065c626122a89920d8f04b5e43e41fe4eb64595e Mon Sep 17 00:00:00 2001 From: delphis-bot Date: Thu, 18 Jul 2024 09:46:41 +0000 Subject: [PATCH 04/12] [automated] Create package recipe from SSF files --- .../2023_Salazar_MachuPicchu.config | 40 +++++++++++++ .../2023_Salazar_MachuPicchu.tsv | 57 +++++++++++++++++++ .../2023_Salazar_MachuPicchu.tsv_patch.sh | 45 +++++++++++++++ .../script_versions.txt | 2 + 4 files changed, 144 insertions(+) create mode 100644 packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.config create mode 100644 packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.tsv create mode 100755 packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.tsv_patch.sh create mode 100644 packages/2023_Salazar_MachuPicchu/script_versions.txt diff --git a/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.config b/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.config new file mode 100644 index 0000000..7fe6a40 --- /dev/null +++ b/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.config @@ -0,0 +1,40 @@ +// Keep track of config versions +config_template_version='0.3.0dev' +package_config_version='0.3.0dev' +minotaur_config_base='https://raw.githubusercontent.com/poseidon-framework/poseidon-eager/main/conf' + +// This configuration file is designed to be a used with the nf-core/eager pipeline. +// Instead of having to specify all other configurations for the Minotaur pipeline +// on runtime, they are all contained in this file and loaded automatically upon +// specifying this config file during runtime. Additionally, any parameters that +// need to be altered from the defaults can be specified here. +// +// The intention is to make it easy for users to understand and reproduce the output +// from processing with the Minotaur workflow processing from the contents of a +// single file. + +// Load configuration profiles. They are loaded from the minotaur_config_base URL, main branch. +includeConfig "${minotaur_config_base}/EVA_cluster.config" // Cluster-specific configurations for nf-core/eager execution at MPI-EVA +includeConfig "${minotaur_config_base}/Minotaur.config" // Default nf-core/eager parameters for Minotaur processing. + +// The following config file specifies BED files for on-target endogenous DNA calculation and mean coverage as well as pseudohaploid genotyping. +// TODO: Select the appropriate config for the CaptureType of the package. +includeConfig "${minotaur_config_base}/CaptureType_profiles/1240K.config" + +params { + // Keep track of config file versions used when processing + config_profile_description = "${config_profile_description}\n - config_template_version: ${config_template_version}\n - package_config_version: ${package_config_version}" + config_profile_contact = "Thiseas C. Lamnidis (@TCLamnidis)" + + /* + TODO: If you need to change any of the default processing parameters for this package + you can specify these parameters below. + Any parameters not specified in any of the config files default to their nf-core/eager default values. + + For information on all available parameters and their default values see: + https://nf-co.re/eager/2.4.6/parameters + + You can see the default values for parameters within poseidon-eager at: + https://github.com/poseidon-framework/poseidon-eager/blob/main/conf/Minotaur.config + */ +} diff --git a/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.tsv b/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.tsv new file mode 100644 index 0000000..06d3138 --- /dev/null +++ b/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.tsv @@ -0,0 +1,57 @@ +Sample_Name Library_ID Lane Colour_Chemistry SeqType Organism Strandedness UDG_Treatment R1 R2 BAM R1_target_file R2_target_file +KCA-3089 KCA-3089_KCA-3089 1 4 SE Homo sapiens (modern human) double half /KCA-3089_KCA-3089_L1_R1.fastq.gz NA NA ERR11518429.fastq.gz NA +KCA-1108 KCA-1108_KCA-1108 1 4 SE Homo sapiens (modern human) double half /KCA-1108_KCA-1108_L1_R1.fastq.gz NA NA ERR11518434.fastq.gz NA +KCA-1364 KCA-1364_KCA-1364 1 4 SE Homo sapiens (modern human) double half /KCA-1364_KCA-1364_L1_R1.fastq.gz NA NA ERR11518435.fastq.gz NA +MP13 MP13_MP13 1 4 PE Homo sapiens (modern human) double half /MP13_MP13_L1_R1.fastq.gz /MP13_MP13_L1_R2.fastq.gz NA ERR11518444.fastq.gz ERR11518444_1.fastq.gz +KMA-28-1 KMA-28-1_KMA-28-1 1 4 SE Homo sapiens (modern human) double half /KMA-28-1_KMA-28-1_L1_R1.fastq.gz NA NA ERR11518463.fastq.gz NA +MP33 MP33_MP33 1 4 PE Homo sapiens (modern human) double half /MP33_MP33_L1_R1.fastq.gz /MP33_MP33_L1_R2.fastq.gz NA ERR11518465.fastq.gz ERR11518465_1.fastq.gz +MP42B MP42B_MP42B 1 4 PE Homo sapiens (modern human) double half /MP42B_MP42B_L1_R1.fastq.gz /MP42B_MP42B_L1_R2.fastq.gz NA ERR11518471.fastq.gz ERR11518471_1.fastq.gz +MP42A MP42A_MP42A 1 4 PE Homo sapiens (modern human) double half /MP42A_MP42A_L1_R1.fastq.gz /MP42A_MP42A_L1_R2.fastq.gz NA ERR11518472.fastq.gz ERR11518472_1.fastq.gz +MP48B MP48B_MP48B 1 4 PE Homo sapiens (modern human) double half /MP48B_MP48B_L1_R1.fastq.gz /MP48B_MP48B_L1_R2.fastq.gz NA ERR11518477.fastq.gz ERR11518477_1.fastq.gz +MP50A MP50A_MP50A 1 4 PE Homo sapiens (modern human) double half /MP50A_MP50A_L1_R1.fastq.gz /MP50A_MP50A_L1_R2.fastq.gz NA ERR11518484.fastq.gz ERR11518484_1.fastq.gz +MP4f MP4f_MP4f 1 4 PE Homo sapiens (modern human) double half /MP4f_MP4f_L1_R1.fastq.gz /MP4f_MP4f_L1_R2.fastq.gz NA ERR11518485.fastq.gz ERR11518485_1.fastq.gz +MP4i MP4i_MP4i 1 4 PE Homo sapiens (modern human) double half /MP4i_MP4i_L1_R1.fastq.gz /MP4i_MP4i_L1_R2.fastq.gz NA ERR11518489.fastq.gz ERR11518489_1.fastq.gz +MP5A MP5A_MP5A 1 4 PE Homo sapiens (modern human) double half /MP5A_MP5A_L1_R1.fastq.gz /MP5A_MP5A_L1_R2.fastq.gz NA ERR11518495.fastq.gz ERR11518495_1.fastq.gz +MP65B MP65B_MP65B 1 4 PE Homo sapiens (modern human) double half /MP65B_MP65B_L1_R1.fastq.gz /MP65B_MP65B_L1_R2.fastq.gz NA ERR11518496.fastq.gz ERR11518496_1.fastq.gz +MP27 MP27_MP27 1 4 PE Homo sapiens (modern human) double half /MP27_MP27_L1_R1.fastq.gz /MP27_MP27_L1_R2.fastq.gz NA ERR11518499.fastq.gz ERR11518499_1.fastq.gz +OTT-1144 OTT-1144_OTT-1144 1 4 SE Homo sapiens (modern human) double half /OTT-1144_OTT-1144_L1_R1.fastq.gz NA NA ERR11518523.fastq.gz NA +MP61 MP61_MP61 1 4 PE Homo sapiens (modern human) double half /MP61_MP61_L1_R1.fastq.gz /MP61_MP61_L1_R2.fastq.gz NA ERR11518546.fastq.gz ERR11518546_1.fastq.gz +QKI-21-1 QKI-21-1_QKI-21-1 1 4 SE Homo sapiens (modern human) double half /QKI-21-1_QKI-21-1_L1_R1.fastq.gz NA NA ERR11518553.fastq.gz NA +MP31A MP31A_MP31A 1 4 PE Homo sapiens (modern human) double half /MP31A_MP31A_L1_R1.fastq.gz /MP31A_MP31A_L1_R2.fastq.gz NA ERR11518458.fastq.gz ERR11518458_1.fastq.gz +KMA-15A-1 KMA-15A-1_KMA-15A-1 1 4 SE Homo sapiens (modern human) double half /KMA-15A-1_KMA-15A-1_L1_R1.fastq.gz NA NA ERR11518461.fastq.gz NA +MP45A MP45A_MP45A 1 4 PE Homo sapiens (modern human) double half /MP45A_MP45A_L1_R1.fastq.gz /MP45A_MP45A_L1_R2.fastq.gz NA ERR11518475.fastq.gz ERR11518475_1.fastq.gz +MP4E MP4E_MP4E 1 4 PE Homo sapiens (modern human) double half /MP4E_MP4E_L1_R1.fastq.gz /MP4E_MP4E_L1_R2.fastq.gz NA ERR11518480.fastq.gz ERR11518480_1.fastq.gz +MP4D MP4D_MP4D 1 4 PE Homo sapiens (modern human) double half /MP4D_MP4D_L1_R1.fastq.gz /MP4D_MP4D_L1_R2.fastq.gz NA ERR11518481.fastq.gz ERR11518481_1.fastq.gz +MP53A MP53A_MP53A 1 4 PE Homo sapiens (modern human) double half /MP53A_MP53A_L1_R1.fastq.gz /MP53A_MP53A_L1_R2.fastq.gz NA ERR11518486.fastq.gz ERR11518486_1.fastq.gz +MP55 MP55_MP55 1 4 PE Homo sapiens (modern human) double half /MP55_MP55_L1_R1.fastq.gz /MP55_MP55_L1_R2.fastq.gz NA ERR11518487.fastq.gz ERR11518487_1.fastq.gz +MP78A MP78A_MP78A 1 4 PE Homo sapiens (modern human) double half /MP78A_MP78A_L1_R1.fastq.gz /MP78A_MP78A_L1_R2.fastq.gz NA ERR11518501.fastq.gz ERR11518501_1.fastq.gz +MP84A MP84A_MP84A 1 4 PE Homo sapiens (modern human) double half /MP84A_MP84A_L1_R1.fastq.gz /MP84A_MP84A_L1_R2.fastq.gz NA ERR11518514.fastq.gz ERR11518514_1.fastq.gz +QKI-809 QKI-809_QKI-809 1 4 SE Homo sapiens (modern human) double half /QKI-809_QKI-809_L1_R1.fastq.gz NA NA ERR11518566.fastq.gz NA +QKI-9-3 QKI-9-3_QKI-9-3 1 4 SE Homo sapiens (modern human) double half /QKI-9-3_QKI-9-3_L1_R1.fastq.gz NA NA ERR11518572.fastq.gz NA +SHN-575 SHN-575_SHN-575 1 4 SE Homo sapiens (modern human) double half /SHN-575_SHN-575_L1_R1.fastq.gz NA NA ERR11518597.fastq.gz NA +KCA-1298 KCA-1298_KCA-1298 1 4 SE Homo sapiens (modern human) double half /KCA-1298_KCA-1298_L1_R1.fastq.gz NA NA ERR11518432.fastq.gz NA +CCA-7-2 CCA-7-2_CCA-7-2 1 4 SE Homo sapiens (modern human) double half /CCA-7-2_CCA-7-2_L1_R1.fastq.gz NA NA ERR11518440.fastq.gz NA +MP107B MP107B_MP107B 1 4 PE Homo sapiens (modern human) double half /MP107B_MP107B_L1_R1.fastq.gz /MP107B_MP107B_L1_R2.fastq.gz NA ERR11518443.fastq.gz ERR11518443_1.fastq.gz +MP23 MP23_MP23 1 4 PE Homo sapiens (modern human) double half /MP23_MP23_L1_R1.fastq.gz /MP23_MP23_L1_R2.fastq.gz NA ERR11518448.fastq.gz ERR11518448_1.fastq.gz +KMA-2-2 KMA-2-2_KMA-2-2 1 4 SE Homo sapiens (modern human) double half /KMA-2-2_KMA-2-2_L1_R1.fastq.gz NA NA ERR11518456.fastq.gz NA +MP32 MP32_MP32 1 4 PE Homo sapiens (modern human) double half /MP32_MP32_L1_R1.fastq.gz /MP32_MP32_L1_R2.fastq.gz NA ERR11518466.fastq.gz ERR11518466_1.fastq.gz +KMA-19-1 KMA-19-1_KMA-19-1 1 4 SE Homo sapiens (modern human) double half /KMA-19-1_KMA-19-1_L1_R1.fastq.gz NA NA ERR11518467.fastq.gz NA +MP42C MP42C_MP42C 1 4 PE Homo sapiens (modern human) double half /MP42C_MP42C_L1_R1.fastq.gz /MP42C_MP42C_L1_R2.fastq.gz NA ERR11518469.fastq.gz ERR11518469_1.fastq.gz +MP4B MP4B_MP4B 1 4 PE Homo sapiens (modern human) double half /MP4B_MP4B_L1_R1.fastq.gz /MP4B_MP4B_L1_R2.fastq.gz NA ERR11518478.fastq.gz ERR11518478_1.fastq.gz +MP51 MP51_MP51 1 4 PE Homo sapiens (modern human) double half /MP51_MP51_L1_R1.fastq.gz /MP51_MP51_L1_R2.fastq.gz NA ERR11518493.fastq.gz ERR11518493_1.fastq.gz +MP71 MP71_MP71 1 4 PE Homo sapiens (modern human) double half /MP71_MP71_L1_R1.fastq.gz /MP71_MP71_L1_R2.fastq.gz NA ERR11518498.fastq.gz ERR11518498_1.fastq.gz +MP77A MP77A_MP77A 1 4 PE Homo sapiens (modern human) double half /MP77A_MP77A_L1_R1.fastq.gz /MP77A_MP77A_L1_R2.fastq.gz NA ERR11518500.fastq.gz ERR11518500_1.fastq.gz +MP82 MP82_MP82 1 4 PE Homo sapiens (modern human) double half /MP82_MP82_L1_R1.fastq.gz /MP82_MP82_L1_R2.fastq.gz NA ERR11518502.fastq.gz ERR11518502_1.fastq.gz +MP80 MP80_MP80 1 4 PE Homo sapiens (modern human) double half /MP80_MP80_L1_R1.fastq.gz /MP80_MP80_L1_R2.fastq.gz NA ERR11518503.fastq.gz ERR11518503_1.fastq.gz +MP84C MP84C_MP84C 1 4 PE Homo sapiens (modern human) double half /MP84C_MP84C_L1_R1.fastq.gz /MP84C_MP84C_L1_R2.fastq.gz NA ERR11518512.fastq.gz ERR11518512_1.fastq.gz +OTT-1160 OTT-1160_OTT-1160 1 4 SE Homo sapiens (modern human) double half /OTT-1160_OTT-1160_L1_R1.fastq.gz NA NA ERR11518538.fastq.gz NA +OTT-1165 OTT-1165_OTT-1165 1 4 SE Homo sapiens (modern human) double half /OTT-1165_OTT-1165_L1_R1.fastq.gz NA NA ERR11518543.fastq.gz NA +MP63 MP63_MP63 1 4 PE Homo sapiens (modern human) double half /MP63_MP63_L1_R1.fastq.gz /MP63_MP63_L1_R2.fastq.gz NA ERR11518550.fastq.gz ERR11518550_1.fastq.gz +OTT-1174 OTT-1174_OTT-1174 1 4 SE Homo sapiens (modern human) double half /OTT-1174_OTT-1174_L1_R1.fastq.gz NA NA ERR11518552.fastq.gz NA +QKI-4 QKI-4_QKI-4 1 4 SE Homo sapiens (modern human) double half /QKI-4_QKI-4_L1_R1.fastq.gz NA NA ERR11518562.fastq.gz NA +OTT-1187 OTT-1187_OTT-1187 1 4 SE Homo sapiens (modern human) double half /OTT-1187_OTT-1187_L1_R1.fastq.gz NA NA ERR11518565.fastq.gz NA +SHN-212 SHN-212_SHN-212 1 4 SE Homo sapiens (modern human) double half /SHN-212_SHN-212_L1_R1.fastq.gz NA NA ERR11518568.fastq.gz NA +SHN-355 SHN-355_SHN-355 1 4 SE Homo sapiens (modern human) double half /SHN-355_SHN-355_L1_R1.fastq.gz NA NA ERR11518578.fastq.gz NA +SHN-492 SHN-492_SHN-492 1 4 SE Homo sapiens (modern human) double half /SHN-492_SHN-492_L1_R1.fastq.gz NA NA ERR11518582.fastq.gz NA +SHN-902 SHN-902_SHN-902 1 4 SE Homo sapiens (modern human) double half /SHN-902_SHN-902_L1_R1.fastq.gz NA NA ERR11518584.fastq.gz NA +MP3a MP3a_MP3a 1 4 PE Homo sapiens (modern human) double half /MP3a_MP3a_L1_R1.fastq.gz /MP3a_MP3a_L1_R2.fastq.gz NA ERR11518632.fastq.gz ERR11518632_1.fastq.gz diff --git a/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.tsv_patch.sh b/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.tsv_patch.sh new file mode 100755 index 0000000..422e836 --- /dev/null +++ b/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.tsv_patch.sh @@ -0,0 +1,45 @@ +#!/usr/bin/env bash +set -uo pipefail ## Pipefail, complain on new unassigned variables. + +## Track the version of the TSV_patch template used +VERSION='0.2.0dev' + +## This script is applied to the eager input TSV file locally to edit the dummy +## path to the fastQ files added by `create_eager_input.sh` to a real local +## path provided as a positional argument. Any further local tweaks to the +## TSV before running eager should be added below that in the form of bash +## commands to aid in reproducibility. + +## usage tsv_patch.sh + +local_data_dir="$(readlink -f ${1})" +input_tsv="$(readlink -f ${2})" +output_tsv="$(dirname ${local_data_dir})/$(basename -s ".tsv" ${input_tsv}).finalised.tsv" +columns_to_keep=("Sample_Name" "Library_ID" "Lane" "Colour_Chemistry" "SeqType" "Organism" "Strandedness" "UDG_Treatment" "R1" "R2" "BAM") +source $(dirname ${2})/../../scripts/source_me.sh ## Load helper functions + +## Index non-proliferated columns and exclude them from the finalised TSV +cut_selector='' +tsv_header=($(head -n1 ${input_tsv})) +for col_name in ${columns_to_keep[@]}; do + let idx=$(get_index_of ${col_name} "${columns_to_keep[@]}")+1 ## awk uses 1-based indexing + if [[ ! ${idx} -eq -1 ]]; then + cut_selector+="${idx}," + fi +done + +## Remove added columns, and put columns in right order +cut -f ${cut_selector%,} ${input_tsv} > ${output_tsv} +sed -i -e "s||${local_data_dir}|g" ${output_tsv} + +## Any further commands to edit the file before finalisation should be added below as shown +# sed -ie 's/replace_this/with_this/g' ${output_tsv} + +## Keep track of versions +version_file="$(dirname ${input_tsv})/script_versions.txt" +## Remove versions from older run if there +grep -v -F -e "$(basename ${0})" -e "source_me.sh for final TSV" ${version_file} >${version_file}.new +## Then add new versions +echo -e "$(basename ${0}):\t${VERSION}" >> ${version_file}.new +echo -e "source_me.sh for final TSV:\t${HELPER_FUNCTION_VERSION}" >>${version_file}.new +mv ${version_file}.new ${version_file} diff --git a/packages/2023_Salazar_MachuPicchu/script_versions.txt b/packages/2023_Salazar_MachuPicchu/script_versions.txt new file mode 100644 index 0000000..be6857b --- /dev/null +++ b/packages/2023_Salazar_MachuPicchu/script_versions.txt @@ -0,0 +1,2 @@ +create_eager_input.sh: 0.2.1dev +source_me.sh for initial TSV: 0.2.1dev From 0cf2483cdbdfd190cc0c5101b718a42144432728 Mon Sep 17 00:00:00 2001 From: "Thiseas C. Lamnidis" Date: Thu, 1 Aug 2024 14:27:33 +0200 Subject: [PATCH 05/12] add gitignore --- .gitignore | 0 packages/2020_Bongers_SouthPeru/script_versions.txt | 5 +++++ packages/2020_Margaryan_Viking/script_versions.txt | 3 +++ packages/2021_CarlhoffNature/script_versions.txt | 5 +++++ packages/2021_PattersonNature/script_versions.txt | 5 +++++ packages/2022_Fischer_Gauls/script_versions.txt | 5 +++++ packages/2023_OlaldeCarrion_Roman/script_versions.txt | 5 +++++ packages/2023_Peltola_VolgaOka/script_versions.txt | 5 +++++ packages/2023_VillaIslas_Science/script_versions.txt | 5 +++++ 9 files changed, 38 insertions(+) create mode 100644 .gitignore diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..e69de29 diff --git a/packages/2020_Bongers_SouthPeru/script_versions.txt b/packages/2020_Bongers_SouthPeru/script_versions.txt index be6857b..d9bb135 100644 --- a/packages/2020_Bongers_SouthPeru/script_versions.txt +++ b/packages/2020_Bongers_SouthPeru/script_versions.txt @@ -1,2 +1,7 @@ create_eager_input.sh: 0.2.1dev source_me.sh for initial TSV: 0.2.1dev +download_ena_data.py: 0.3.0dev +validate_downloaded_data.sh: 0.2.2dev +source_me.sh for data validation: 0.2.1dev +2020_Bongers_SouthPeru.tsv_patch.sh: 0.2.1dev +source_me.sh for final TSV: 0.2.1dev diff --git a/packages/2020_Margaryan_Viking/script_versions.txt b/packages/2020_Margaryan_Viking/script_versions.txt index be6857b..b2c9d0a 100644 --- a/packages/2020_Margaryan_Viking/script_versions.txt +++ b/packages/2020_Margaryan_Viking/script_versions.txt @@ -1,2 +1,5 @@ create_eager_input.sh: 0.2.1dev source_me.sh for initial TSV: 0.2.1dev +download_ena_data.py: 0.3.0dev +2020_Margaryan_Viking.tsv_patch.sh: 0.2.1dev +source_me.sh for final TSV: 0.2.1dev diff --git a/packages/2021_CarlhoffNature/script_versions.txt b/packages/2021_CarlhoffNature/script_versions.txt index be6857b..dd83cd3 100644 --- a/packages/2021_CarlhoffNature/script_versions.txt +++ b/packages/2021_CarlhoffNature/script_versions.txt @@ -1,2 +1,7 @@ create_eager_input.sh: 0.2.1dev source_me.sh for initial TSV: 0.2.1dev +download_ena_data.py: 0.2.0dev +validate_downloaded_data.sh: 0.2.2dev +source_me.sh for data validation: 0.2.1dev +2021_CarlhoffNature.tsv_patch.sh: 0.2.1dev +source_me.sh for final TSV: 0.2.1dev diff --git a/packages/2021_PattersonNature/script_versions.txt b/packages/2021_PattersonNature/script_versions.txt index be6857b..e74128d 100644 --- a/packages/2021_PattersonNature/script_versions.txt +++ b/packages/2021_PattersonNature/script_versions.txt @@ -1,2 +1,7 @@ create_eager_input.sh: 0.2.1dev source_me.sh for initial TSV: 0.2.1dev +download_ena_data.py: 0.3.0dev +validate_downloaded_data.sh: 0.2.2dev +source_me.sh for data validation: 0.2.1dev +2021_PattersonNature.tsv_patch.sh: 0.2.1dev +source_me.sh for final TSV: 0.2.1dev diff --git a/packages/2022_Fischer_Gauls/script_versions.txt b/packages/2022_Fischer_Gauls/script_versions.txt index be6857b..4914b12 100644 --- a/packages/2022_Fischer_Gauls/script_versions.txt +++ b/packages/2022_Fischer_Gauls/script_versions.txt @@ -1,2 +1,7 @@ create_eager_input.sh: 0.2.1dev source_me.sh for initial TSV: 0.2.1dev +download_ena_data.py: 0.3.0dev +validate_downloaded_data.sh: 0.2.2dev +source_me.sh for data validation: 0.2.1dev +2022_Fischer_Gauls.tsv_patch.sh: 0.2.1dev +source_me.sh for final TSV: 0.2.1dev diff --git a/packages/2023_OlaldeCarrion_Roman/script_versions.txt b/packages/2023_OlaldeCarrion_Roman/script_versions.txt index be6857b..8fffef3 100644 --- a/packages/2023_OlaldeCarrion_Roman/script_versions.txt +++ b/packages/2023_OlaldeCarrion_Roman/script_versions.txt @@ -1,2 +1,7 @@ create_eager_input.sh: 0.2.1dev source_me.sh for initial TSV: 0.2.1dev +download_ena_data.py: 0.2.0dev +validate_downloaded_data.sh: 0.2.2dev +source_me.sh for data validation: 0.2.1dev +2023_OlaldeCarrion_Roman.tsv_patch.sh: 0.2.1dev +source_me.sh for final TSV: 0.2.1dev diff --git a/packages/2023_Peltola_VolgaOka/script_versions.txt b/packages/2023_Peltola_VolgaOka/script_versions.txt index be6857b..f37667d 100644 --- a/packages/2023_Peltola_VolgaOka/script_versions.txt +++ b/packages/2023_Peltola_VolgaOka/script_versions.txt @@ -1,2 +1,7 @@ create_eager_input.sh: 0.2.1dev source_me.sh for initial TSV: 0.2.1dev +download_ena_data.py: 0.3.0dev +validate_downloaded_data.sh: 0.2.2dev +source_me.sh for data validation: 0.2.1dev +2023_Peltola_VolgaOka.tsv_patch.sh: 0.2.1dev +source_me.sh for final TSV: 0.2.1dev diff --git a/packages/2023_VillaIslas_Science/script_versions.txt b/packages/2023_VillaIslas_Science/script_versions.txt index be6857b..a94474c 100644 --- a/packages/2023_VillaIslas_Science/script_versions.txt +++ b/packages/2023_VillaIslas_Science/script_versions.txt @@ -1,2 +1,7 @@ create_eager_input.sh: 0.2.1dev source_me.sh for initial TSV: 0.2.1dev +download_ena_data.py: 0.3.0dev +validate_downloaded_data.sh: 0.2.2dev +source_me.sh for data validation: 0.2.1dev +2023_VillaIslas_Science.tsv_patch.sh: 0.2.1dev +source_me.sh for final TSV: 0.2.1dev From 58fb2d4c3e4c8d687d4f198d26dbba854b3fdd92 Mon Sep 17 00:00:00 2001 From: "Thiseas C. Lamnidis" Date: Thu, 1 Aug 2024 14:33:17 +0200 Subject: [PATCH 06/12] Update config for renewed processing. --- .../2020_Nagele_Caribbean.config | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.config b/packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.config index 1b03016..ca10f8b 100644 --- a/packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.config +++ b/packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.config @@ -1,6 +1,8 @@ // Keep track of config versions -config_template_version='0.2.0dev' -package_config_version='0.2.0dev' +minotaur_release='0.3.0dev' // The release tag of the poseidon-eager repository used for processing and config file retrieval +config_template_version='0.3.0dev' +package_config_version='0.3.0dev' +minotaur_config_base="https://raw.githubusercontent.com/poseidon-framework/poseidon-eager/${minotaur_release}/conf" // This configuration file is designed to be a used with the nf-core/eager pipeline. // Instead of having to specify all other configurations for the Minotaur pipeline @@ -12,17 +14,17 @@ package_config_version='0.2.0dev' // from processing with the Minotaur workflow processing from the contents of a // single file. -// Load configuration profiles -includeConfig "../../conf/EVA_cluster.config" // Cluster-specific configurations for nf-core/eager execution at MPI-EVA -includeConfig "../../conf/Minotaur.config" // Default nf-core/eager parameters for Minotaur processing. +// Load configuration profiles. They are loaded from the minotaur_config_base URL, main branch. +includeConfig "${minotaur_config_base}/EVA_cluster.config" // Cluster-specific configurations for nf-core/eager execution at MPI-EVA +includeConfig "${minotaur_config_base}/Minotaur.config" // Default nf-core/eager parameters for Minotaur processing. // The following config file specifies BED files for on-target endogenous DNA calculation and mean coverage as well as pseudohaploid genotyping. // TODO: Select the appropriate config for the CaptureType of the package. -includeConfig '../../conf/CaptureType_profiles/1240K.config' +includeConfig "${minotaur_config_base}/CaptureType_profiles/1240K.config" params { // Keep track of config file versions used when processing - config_profile_description = "${config_profile_description}\nconfig_template_version: ${config_template_version}\npackage_config_version: ${package_config_version}" + config_profile_description = "${config_profile_description}\n - config_template_version: ${config_template_version}\n - package_config_version: ${package_config_version}" config_profile_contact = "Thiseas C. Lamnidis (@TCLamnidis)" /* From 69f0d139257f6a2078796caa507efc701fa836aa Mon Sep 17 00:00:00 2001 From: Thiseas Christos Lamnidis Date: Thu, 15 Aug 2024 15:27:23 +0200 Subject: [PATCH 07/12] Update tsv_patch --- .../2023_Salazar_MachuPicchu.tsv_patch.sh | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.tsv_patch.sh b/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.tsv_patch.sh index 422e836..a73f9af 100755 --- a/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.tsv_patch.sh +++ b/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.tsv_patch.sh @@ -2,7 +2,7 @@ set -uo pipefail ## Pipefail, complain on new unassigned variables. ## Track the version of the TSV_patch template used -VERSION='0.2.0dev' +VERSION='0.2.1dev' ## This script is applied to the eager input TSV file locally to edit the dummy ## path to the fastQ files added by `create_eager_input.sh` to a real local @@ -10,13 +10,13 @@ VERSION='0.2.0dev' ## TSV before running eager should be added below that in the form of bash ## commands to aid in reproducibility. -## usage tsv_patch.sh +## usage tsv_patch.sh local_data_dir="$(readlink -f ${1})" input_tsv="$(readlink -f ${2})" output_tsv="$(dirname ${local_data_dir})/$(basename -s ".tsv" ${input_tsv}).finalised.tsv" columns_to_keep=("Sample_Name" "Library_ID" "Lane" "Colour_Chemistry" "SeqType" "Organism" "Strandedness" "UDG_Treatment" "R1" "R2" "BAM") -source $(dirname ${2})/../../scripts/source_me.sh ## Load helper functions +source $(readlink -f ${3}) ## Path to helper function script should be provided as 3rd argument. https://github.com/poseidon-framework/poseidon-eager/blob/main/scripts/source_me.sh ## Index non-proliferated columns and exclude them from the finalised TSV cut_selector='' From 34aaee49ef8f8970e4b4b9f69866eacde4448e8d Mon Sep 17 00:00:00 2001 From: Thiseas Christos Lamnidis Date: Wed, 4 Sep 2024 13:08:16 +0200 Subject: [PATCH 08/12] Update functions to handle BAMs with collapsed reads. --- scripts/delphis-bot_scripts/source_me.sh | 46 +++++++++++++++++------- 1 file changed, 33 insertions(+), 13 deletions(-) diff --git a/scripts/delphis-bot_scripts/source_me.sh b/scripts/delphis-bot_scripts/source_me.sh index 8922a6a..628e616 100644 --- a/scripts/delphis-bot_scripts/source_me.sh +++ b/scripts/delphis-bot_scripts/source_me.sh @@ -1,5 +1,5 @@ #!/usr/bin/env bash -HELPER_FUNCTION_VERSION='0.2.1dev' +HELPER_FUNCTION_VERSION='0.2.2dev' ## Print coloured messages to stderr # errecho -r will print in red @@ -108,7 +108,7 @@ function number_of_entries() { ## MUST be a single character ## is 0-based # usage: pull_by_index -# number_of_entries ';' 'ABC001;ABC001_subset' 1 ## Returns 'ABC001' +# pull_by_index ';' 'ABC001;ABC001_subset' 1 ## Returns 'ABC001_subset' function pull_by_index() { local delim local value @@ -234,16 +234,25 @@ function r1_r2_from_ena_fastq() { local r1 local r2 local seq_type + local n_entries value="${1}" - r1=$(basename "$(pull_by_index ';' ${value} 0)") - r2=$(basename "$(pull_by_index ';' ${value} 1)") - seq_type="PE" - ## If no R2, then SE - if [[ "${r2}" == '' ]]; then + ## BAMs containing collapsed PE reads will have 3 entries in the ENA (merged, R1 unmerged, R2 unmerged), but we only need the first (merged reads). + n_entries=$(number_of_entries ';' ${value}) + + r1=$(basename "$(pull_by_index ';' ${value} 0)") + if [[ ${n_entries} -eq 2 ]]; then + ## If there are two entries, then it's PE + r2=$(basename "$(pull_by_index ';' ${value} 1)") + seq_type="PE" + elif [[ ${n_entries} -eq 1 || ${n_entries} -eq 3 ]]; then + ## If there is only one entry, then it's SE. With three, it is a BAM with collapsed reads, so keep only merged reads (treat as SE). r2="NA" seq_type="SE" + else + errecho -r "Unexpected number of entries in fastq_ftp field: ${value}." + exit 1 fi echo "${seq_type} ${r1} ${r2}" @@ -264,16 +273,22 @@ function dummy_r1_r2_from_ena_fastq() { prefix="${1}" out_fn_prefix="${2}" value="${3}" + + ## BAMs containing collapsed PE reads will have 3 entries in the ENA (merged, R1 unmerged, R2 unmerged), but we only need the first (merged reads). n_entries=$(number_of_entries ';' ${value}) r1="${prefix}/${out_fn_prefix}_R1.fastq.gz" - if [[ ${n_entries} -gt 1 ]]; then + if [[ ${n_entries} -eq 2 ]]; then + ## If there are two entries, then it's PE r2="${prefix}/${out_fn_prefix}_R2.fastq.gz" seq_type="PE" - else - ## If no R2, then SE + elif [[ ${n_entries} -eq 1 || ${n_entries} -eq 3 ]]; then + ## If there is only one entry, then it's SE. With three, it is a BAM with collapsed reads, so keep only merged reads (treat as SE). r2="NA" seq_type="SE" + else + errecho -r "Unexpected number of entries in fastq_ftp field: ${value}." + exit 1 fi echo "${seq_type} ${r1} ${r2}" @@ -299,19 +314,24 @@ function symlink_names_from_ena_fastq() { out_fn_prefix="${3}" value="${4}" + ## BAMs containing collapsed PE reads will have 3 entries in the ENA (merged, R1 unmerged, R2 unmerged), but we only need the first (merged reads). n_entries=$(number_of_entries ';' ${value}) r1="${download_path}/$(basename $(pull_by_index ';' ${value} 0))" r1_symlink="${output_path}/${out_fn_prefix}_R1.fastq.gz" - if [[ ${n_entries} -gt 1 ]]; then + if [[ ${n_entries} -eq 2 ]]; then + ## If there are two entries, then it's PE r2="${download_path}/$(basename $(pull_by_index ';' ${value} 1))" r2_symlink="${output_path}/${out_fn_prefix}_R2.fastq.gz" seq_type="PE" - else - ## If no R2, then SE + elif [[ ${n_entries} -eq 1 || ${n_entries} -eq 3 ]]; then + ## If there is only one entry, then it's SE. With three, it is a BAM with collapsed reads, so keep only merged reads (treat as SE). r2="NA" r2_symlink="NA" seq_type="SE" + else + errecho -r "Unexpected number of entries in fastq_ftp field: ${value}." + exit 1 fi echo "${seq_type} ${r1} ${r1_symlink} ${r2} ${r2_symlink}" From 36fb9537926eb348350ec5e67d5aa1656e2845ac Mon Sep 17 00:00:00 2001 From: Thiseas Christos Lamnidis Date: Wed, 4 Sep 2024 13:41:56 +0200 Subject: [PATCH 09/12] Comment out potentially unused functions for testing --- scripts/delphis-bot_scripts/source_me.sh | 193 ++++++++++++----------- 1 file changed, 97 insertions(+), 96 deletions(-) diff --git a/scripts/delphis-bot_scripts/source_me.sh b/scripts/delphis-bot_scripts/source_me.sh index 628e616..526fefa 100644 --- a/scripts/delphis-bot_scripts/source_me.sh +++ b/scripts/delphis-bot_scripts/source_me.sh @@ -1,5 +1,5 @@ #!/usr/bin/env bash -HELPER_FUNCTION_VERSION='0.2.2dev' +HELPER_FUNCTION_VERSION='0.2.3dev' ## Print coloured messages to stderr # errecho -r will print in red @@ -121,35 +121,6 @@ function pull_by_index() { echo ${value[${index}]} } -## Function to check if all items of array X are in array Y, and return any entries exclusive to X. -# all_x_in_y X1 [X2 X3 ...] Y1 [Y2 Y3 ...] -# Returns: A space separated list of exclusive elements in X -function all_x_in_y() { - local length_x - local x - local length_y - local y - local exclusive_entries - local xid - - let length_x=${1} - shift 1 - x=("${@:1:${length_x}}") - shift ${length_x} - let length_y=${1} - shift 1 - y=("${@:1:${length_y}}") - exclusive_entries=() - - for xid in ${x[@]}; do - if [[ $(count_instances ${xid} "${y[@]}") == 0 ]]; then - exclusive_entries+=("${xid}") - fi - done - - echo "${exclusive_entries[@]}" -} - ## Function to return udg treatment based on janno entry # usage: infer_library_udg 'half;minus;plus' 0 # The second argument (index) is 0-based @@ -294,72 +265,102 @@ function dummy_r1_r2_from_ena_fastq() { echo "${seq_type} ${r1} ${r2}" } -## Function to create R1 and R2 columns from ena_table fastq_fn entries -# usage: symlink_names_from_ena_fastq -# Returns: a space separated list of seq_type R1 R1_symlink R2 R2_symlink -function symlink_names_from_ena_fastq() { - local download_path - local output_path - local out_fn_prefix - local value - local r1 - local r1_symlink - local r2 - local r2_symlink - local seq_type - local n_entries - - download_path="${1}" - output_path="${2}" - out_fn_prefix="${3}" - value="${4}" - - ## BAMs containing collapsed PE reads will have 3 entries in the ENA (merged, R1 unmerged, R2 unmerged), but we only need the first (merged reads). - n_entries=$(number_of_entries ';' ${value}) - - r1="${download_path}/$(basename $(pull_by_index ';' ${value} 0))" - r1_symlink="${output_path}/${out_fn_prefix}_R1.fastq.gz" - if [[ ${n_entries} -eq 2 ]]; then - ## If there are two entries, then it's PE - r2="${download_path}/$(basename $(pull_by_index ';' ${value} 1))" - r2_symlink="${output_path}/${out_fn_prefix}_R2.fastq.gz" - seq_type="PE" - elif [[ ${n_entries} -eq 1 || ${n_entries} -eq 3 ]]; then - ## If there is only one entry, then it's SE. With three, it is a BAM with collapsed reads, so keep only merged reads (treat as SE). - r2="NA" - r2_symlink="NA" - seq_type="SE" - else - errecho -r "Unexpected number of entries in fastq_ftp field: ${value}." - exit 1 - fi - - echo "${seq_type} ${r1} ${r1_symlink} ${r2} ${r2_symlink}" -} - -## Function to create R1 and R2 columns from ena_table fastq_fn entries -# usage: local_r1_r2_from_ena_fastq ${path_to_ena_data} ${fastq_fn} -# Returns: a thrupple of: seq_type R1 R2 -function local_r1_r2_from_ena_fastq() { - local data_path - local value - local r1 - local r2 - local seq_type - - data_path=$1 - value=$2 - r1="${data_path}/${value%%;*}" - r2="${data_path}/${value##*;}" - seq_type="PE" - - if [[ "${r2}" == "${r1}" ]]; then - r2="NA" - seq_type="SE" - fi - - echo "${seq_type} ${r1} ${r2}" -} +# ## NOTE: The following commands will be removed soon. currently commented out for testing. they are used in poseidon-eager only, and need not be here. +# ## Function to check if all items of array X are in array Y, and return any entries exclusive to X. +# # all_x_in_y X1 [X2 X3 ...] Y1 [Y2 Y3 ...] +# # Returns: A space separated list of exclusive elements in X +# function all_x_in_y() { +# local length_x +# local x +# local length_y +# local y +# local exclusive_entries +# local xid + +# let length_x=${1} +# shift 1 +# x=("${@:1:${length_x}}") +# shift ${length_x} +# let length_y=${1} +# shift 1 +# y=("${@:1:${length_y}}") +# exclusive_entries=() + +# for xid in ${x[@]}; do +# if [[ $(count_instances ${xid} "${y[@]}") == 0 ]]; then +# exclusive_entries+=("${xid}") +# fi +# done + +# echo "${exclusive_entries[@]}" +# } + +# ## Function to create R1 and R2 columns from ena_table fastq_fn entries +# # usage: symlink_names_from_ena_fastq +# # Returns: a space separated list of seq_type R1 R1_symlink R2 R2_symlink +# function symlink_names_from_ena_fastq() { +# local download_path +# local output_path +# local out_fn_prefix +# local value +# local r1 +# local r1_symlink +# local r2 +# local r2_symlink +# local seq_type +# local n_entries + +# download_path="${1}" +# output_path="${2}" +# out_fn_prefix="${3}" +# value="${4}" + +# ## BAMs containing collapsed PE reads will have 3 entries in the ENA (merged, R1 unmerged, R2 unmerged), but we only need the first (merged reads). +# n_entries=$(number_of_entries ';' ${value}) + +# r1="${download_path}/$(basename $(pull_by_index ';' ${value} 0))" +# r1_symlink="${output_path}/${out_fn_prefix}_R1.fastq.gz" +# if [[ ${n_entries} -eq 2 ]]; then +# ## If there are two entries, then it's PE +# r2="${download_path}/$(basename $(pull_by_index ';' ${value} 1))" +# r2_symlink="${output_path}/${out_fn_prefix}_R2.fastq.gz" +# seq_type="PE" +# elif [[ ${n_entries} -eq 1 || ${n_entries} -eq 3 ]]; then +# ## If there is only one entry, then it's SE. With three, it is a BAM with collapsed reads, so keep only merged reads (treat as SE). +# r2="NA" +# r2_symlink="NA" +# seq_type="SE" +# else +# errecho -r "Unexpected number of entries in fastq_ftp field: ${value}." +# exit 1 +# fi + +# echo "${seq_type} ${r1} ${r1_symlink} ${r2} ${r2_symlink}" +# } + +# ## Function to create R1 and R2 columns from ena_table fastq_fn entries +# # usage: local_r1_r2_from_ena_fastq ${path_to_ena_data} ${fastq_fn} +# # Returns: a thrupple of: seq_type R1 R2 +# function local_r1_r2_from_ena_fastq() { +# local data_path +# local value +# local r1 +# local r2 +# local seq_type + +# data_path=$1 +# value=$2 +# r1="${data_path}/${value%%;*}" +# r2="${data_path}/${value##*;}" +# seq_type="PE" + +# if [[ "${r2}" == "${r1}" ]]; then +# r2="NA" +# seq_type="SE" +# fi + +# echo "${seq_type} ${r1} ${r2}" +# } ## Function to infer colour chemistry from an ENA-approved instrument model # Usage: infer_colour_chemistry ${instrument_platform} ${instrument_model} From d9a12402ae6519ec7661e8e0770afeed92850f62 Mon Sep 17 00:00:00 2001 From: Thiseas Christos Lamnidis Date: Wed, 4 Sep 2024 14:50:05 +0200 Subject: [PATCH 10/12] Update TSV to only use collapsed read FastQ from BAMs --- .../2023_Salazar_MachuPicchu.tsv | 66 +++++++++---------- .../script_versions.txt | 2 +- 2 files changed, 34 insertions(+), 34 deletions(-) diff --git a/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.tsv b/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.tsv index 06d3138..741df02 100644 --- a/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.tsv +++ b/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.tsv @@ -2,51 +2,51 @@ Sample_Name Library_ID Lane Colour_Chemistry SeqType Organism Strandedness UDG_T KCA-3089 KCA-3089_KCA-3089 1 4 SE Homo sapiens (modern human) double half /KCA-3089_KCA-3089_L1_R1.fastq.gz NA NA ERR11518429.fastq.gz NA KCA-1108 KCA-1108_KCA-1108 1 4 SE Homo sapiens (modern human) double half /KCA-1108_KCA-1108_L1_R1.fastq.gz NA NA ERR11518434.fastq.gz NA KCA-1364 KCA-1364_KCA-1364 1 4 SE Homo sapiens (modern human) double half /KCA-1364_KCA-1364_L1_R1.fastq.gz NA NA ERR11518435.fastq.gz NA -MP13 MP13_MP13 1 4 PE Homo sapiens (modern human) double half /MP13_MP13_L1_R1.fastq.gz /MP13_MP13_L1_R2.fastq.gz NA ERR11518444.fastq.gz ERR11518444_1.fastq.gz +MP13 MP13_MP13 1 4 SE Homo sapiens (modern human) double half /MP13_MP13_L1_R1.fastq.gz NA NA ERR11518444.fastq.gz NA KMA-28-1 KMA-28-1_KMA-28-1 1 4 SE Homo sapiens (modern human) double half /KMA-28-1_KMA-28-1_L1_R1.fastq.gz NA NA ERR11518463.fastq.gz NA -MP33 MP33_MP33 1 4 PE Homo sapiens (modern human) double half /MP33_MP33_L1_R1.fastq.gz /MP33_MP33_L1_R2.fastq.gz NA ERR11518465.fastq.gz ERR11518465_1.fastq.gz -MP42B MP42B_MP42B 1 4 PE Homo sapiens (modern human) double half /MP42B_MP42B_L1_R1.fastq.gz /MP42B_MP42B_L1_R2.fastq.gz NA ERR11518471.fastq.gz ERR11518471_1.fastq.gz -MP42A MP42A_MP42A 1 4 PE Homo sapiens (modern human) double half /MP42A_MP42A_L1_R1.fastq.gz /MP42A_MP42A_L1_R2.fastq.gz NA ERR11518472.fastq.gz ERR11518472_1.fastq.gz -MP48B MP48B_MP48B 1 4 PE Homo sapiens (modern human) double half /MP48B_MP48B_L1_R1.fastq.gz /MP48B_MP48B_L1_R2.fastq.gz NA ERR11518477.fastq.gz ERR11518477_1.fastq.gz -MP50A MP50A_MP50A 1 4 PE Homo sapiens (modern human) double half /MP50A_MP50A_L1_R1.fastq.gz /MP50A_MP50A_L1_R2.fastq.gz NA ERR11518484.fastq.gz ERR11518484_1.fastq.gz -MP4f MP4f_MP4f 1 4 PE Homo sapiens (modern human) double half /MP4f_MP4f_L1_R1.fastq.gz /MP4f_MP4f_L1_R2.fastq.gz NA ERR11518485.fastq.gz ERR11518485_1.fastq.gz -MP4i MP4i_MP4i 1 4 PE Homo sapiens (modern human) double half /MP4i_MP4i_L1_R1.fastq.gz /MP4i_MP4i_L1_R2.fastq.gz NA ERR11518489.fastq.gz ERR11518489_1.fastq.gz -MP5A MP5A_MP5A 1 4 PE Homo sapiens (modern human) double half /MP5A_MP5A_L1_R1.fastq.gz /MP5A_MP5A_L1_R2.fastq.gz NA ERR11518495.fastq.gz ERR11518495_1.fastq.gz -MP65B MP65B_MP65B 1 4 PE Homo sapiens (modern human) double half /MP65B_MP65B_L1_R1.fastq.gz /MP65B_MP65B_L1_R2.fastq.gz NA ERR11518496.fastq.gz ERR11518496_1.fastq.gz -MP27 MP27_MP27 1 4 PE Homo sapiens (modern human) double half /MP27_MP27_L1_R1.fastq.gz /MP27_MP27_L1_R2.fastq.gz NA ERR11518499.fastq.gz ERR11518499_1.fastq.gz +MP33 MP33_MP33 1 4 SE Homo sapiens (modern human) double half /MP33_MP33_L1_R1.fastq.gz NA NA ERR11518465.fastq.gz NA +MP42B MP42B_MP42B 1 4 SE Homo sapiens (modern human) double half /MP42B_MP42B_L1_R1.fastq.gz NA NA ERR11518471.fastq.gz NA +MP42A MP42A_MP42A 1 4 SE Homo sapiens (modern human) double half /MP42A_MP42A_L1_R1.fastq.gz NA NA ERR11518472.fastq.gz NA +MP48B MP48B_MP48B 1 4 SE Homo sapiens (modern human) double half /MP48B_MP48B_L1_R1.fastq.gz NA NA ERR11518477.fastq.gz NA +MP50A MP50A_MP50A 1 4 SE Homo sapiens (modern human) double half /MP50A_MP50A_L1_R1.fastq.gz NA NA ERR11518484.fastq.gz NA +MP4f MP4f_MP4f 1 4 SE Homo sapiens (modern human) double half /MP4f_MP4f_L1_R1.fastq.gz NA NA ERR11518485.fastq.gz NA +MP4i MP4i_MP4i 1 4 SE Homo sapiens (modern human) double half /MP4i_MP4i_L1_R1.fastq.gz NA NA ERR11518489.fastq.gz NA +MP5A MP5A_MP5A 1 4 SE Homo sapiens (modern human) double half /MP5A_MP5A_L1_R1.fastq.gz NA NA ERR11518495.fastq.gz NA +MP65B MP65B_MP65B 1 4 SE Homo sapiens (modern human) double half /MP65B_MP65B_L1_R1.fastq.gz NA NA ERR11518496.fastq.gz NA +MP27 MP27_MP27 1 4 SE Homo sapiens (modern human) double half /MP27_MP27_L1_R1.fastq.gz NA NA ERR11518499.fastq.gz NA OTT-1144 OTT-1144_OTT-1144 1 4 SE Homo sapiens (modern human) double half /OTT-1144_OTT-1144_L1_R1.fastq.gz NA NA ERR11518523.fastq.gz NA -MP61 MP61_MP61 1 4 PE Homo sapiens (modern human) double half /MP61_MP61_L1_R1.fastq.gz /MP61_MP61_L1_R2.fastq.gz NA ERR11518546.fastq.gz ERR11518546_1.fastq.gz +MP61 MP61_MP61 1 4 SE Homo sapiens (modern human) double half /MP61_MP61_L1_R1.fastq.gz NA NA ERR11518546.fastq.gz NA QKI-21-1 QKI-21-1_QKI-21-1 1 4 SE Homo sapiens (modern human) double half /QKI-21-1_QKI-21-1_L1_R1.fastq.gz NA NA ERR11518553.fastq.gz NA -MP31A MP31A_MP31A 1 4 PE Homo sapiens (modern human) double half /MP31A_MP31A_L1_R1.fastq.gz /MP31A_MP31A_L1_R2.fastq.gz NA ERR11518458.fastq.gz ERR11518458_1.fastq.gz +MP31A MP31A_MP31A 1 4 SE Homo sapiens (modern human) double half /MP31A_MP31A_L1_R1.fastq.gz NA NA ERR11518458.fastq.gz NA KMA-15A-1 KMA-15A-1_KMA-15A-1 1 4 SE Homo sapiens (modern human) double half /KMA-15A-1_KMA-15A-1_L1_R1.fastq.gz NA NA ERR11518461.fastq.gz NA -MP45A MP45A_MP45A 1 4 PE Homo sapiens (modern human) double half /MP45A_MP45A_L1_R1.fastq.gz /MP45A_MP45A_L1_R2.fastq.gz NA ERR11518475.fastq.gz ERR11518475_1.fastq.gz -MP4E MP4E_MP4E 1 4 PE Homo sapiens (modern human) double half /MP4E_MP4E_L1_R1.fastq.gz /MP4E_MP4E_L1_R2.fastq.gz NA ERR11518480.fastq.gz ERR11518480_1.fastq.gz -MP4D MP4D_MP4D 1 4 PE Homo sapiens (modern human) double half /MP4D_MP4D_L1_R1.fastq.gz /MP4D_MP4D_L1_R2.fastq.gz NA ERR11518481.fastq.gz ERR11518481_1.fastq.gz -MP53A MP53A_MP53A 1 4 PE Homo sapiens (modern human) double half /MP53A_MP53A_L1_R1.fastq.gz /MP53A_MP53A_L1_R2.fastq.gz NA ERR11518486.fastq.gz ERR11518486_1.fastq.gz -MP55 MP55_MP55 1 4 PE Homo sapiens (modern human) double half /MP55_MP55_L1_R1.fastq.gz /MP55_MP55_L1_R2.fastq.gz NA ERR11518487.fastq.gz ERR11518487_1.fastq.gz -MP78A MP78A_MP78A 1 4 PE Homo sapiens (modern human) double half /MP78A_MP78A_L1_R1.fastq.gz /MP78A_MP78A_L1_R2.fastq.gz NA ERR11518501.fastq.gz ERR11518501_1.fastq.gz -MP84A MP84A_MP84A 1 4 PE Homo sapiens (modern human) double half /MP84A_MP84A_L1_R1.fastq.gz /MP84A_MP84A_L1_R2.fastq.gz NA ERR11518514.fastq.gz ERR11518514_1.fastq.gz +MP45A MP45A_MP45A 1 4 SE Homo sapiens (modern human) double half /MP45A_MP45A_L1_R1.fastq.gz NA NA ERR11518475.fastq.gz NA +MP4E MP4E_MP4E 1 4 SE Homo sapiens (modern human) double half /MP4E_MP4E_L1_R1.fastq.gz NA NA ERR11518480.fastq.gz NA +MP4D MP4D_MP4D 1 4 SE Homo sapiens (modern human) double half /MP4D_MP4D_L1_R1.fastq.gz NA NA ERR11518481.fastq.gz NA +MP53A MP53A_MP53A 1 4 SE Homo sapiens (modern human) double half /MP53A_MP53A_L1_R1.fastq.gz NA NA ERR11518486.fastq.gz NA +MP55 MP55_MP55 1 4 SE Homo sapiens (modern human) double half /MP55_MP55_L1_R1.fastq.gz NA NA ERR11518487.fastq.gz NA +MP78A MP78A_MP78A 1 4 SE Homo sapiens (modern human) double half /MP78A_MP78A_L1_R1.fastq.gz NA NA ERR11518501.fastq.gz NA +MP84A MP84A_MP84A 1 4 SE Homo sapiens (modern human) double half /MP84A_MP84A_L1_R1.fastq.gz NA NA ERR11518514.fastq.gz NA QKI-809 QKI-809_QKI-809 1 4 SE Homo sapiens (modern human) double half /QKI-809_QKI-809_L1_R1.fastq.gz NA NA ERR11518566.fastq.gz NA QKI-9-3 QKI-9-3_QKI-9-3 1 4 SE Homo sapiens (modern human) double half /QKI-9-3_QKI-9-3_L1_R1.fastq.gz NA NA ERR11518572.fastq.gz NA SHN-575 SHN-575_SHN-575 1 4 SE Homo sapiens (modern human) double half /SHN-575_SHN-575_L1_R1.fastq.gz NA NA ERR11518597.fastq.gz NA KCA-1298 KCA-1298_KCA-1298 1 4 SE Homo sapiens (modern human) double half /KCA-1298_KCA-1298_L1_R1.fastq.gz NA NA ERR11518432.fastq.gz NA CCA-7-2 CCA-7-2_CCA-7-2 1 4 SE Homo sapiens (modern human) double half /CCA-7-2_CCA-7-2_L1_R1.fastq.gz NA NA ERR11518440.fastq.gz NA -MP107B MP107B_MP107B 1 4 PE Homo sapiens (modern human) double half /MP107B_MP107B_L1_R1.fastq.gz /MP107B_MP107B_L1_R2.fastq.gz NA ERR11518443.fastq.gz ERR11518443_1.fastq.gz -MP23 MP23_MP23 1 4 PE Homo sapiens (modern human) double half /MP23_MP23_L1_R1.fastq.gz /MP23_MP23_L1_R2.fastq.gz NA ERR11518448.fastq.gz ERR11518448_1.fastq.gz +MP107B MP107B_MP107B 1 4 SE Homo sapiens (modern human) double half /MP107B_MP107B_L1_R1.fastq.gz NA NA ERR11518443.fastq.gz NA +MP23 MP23_MP23 1 4 SE Homo sapiens (modern human) double half /MP23_MP23_L1_R1.fastq.gz NA NA ERR11518448.fastq.gz NA KMA-2-2 KMA-2-2_KMA-2-2 1 4 SE Homo sapiens (modern human) double half /KMA-2-2_KMA-2-2_L1_R1.fastq.gz NA NA ERR11518456.fastq.gz NA -MP32 MP32_MP32 1 4 PE Homo sapiens (modern human) double half /MP32_MP32_L1_R1.fastq.gz /MP32_MP32_L1_R2.fastq.gz NA ERR11518466.fastq.gz ERR11518466_1.fastq.gz +MP32 MP32_MP32 1 4 SE Homo sapiens (modern human) double half /MP32_MP32_L1_R1.fastq.gz NA NA ERR11518466.fastq.gz NA KMA-19-1 KMA-19-1_KMA-19-1 1 4 SE Homo sapiens (modern human) double half /KMA-19-1_KMA-19-1_L1_R1.fastq.gz NA NA ERR11518467.fastq.gz NA -MP42C MP42C_MP42C 1 4 PE Homo sapiens (modern human) double half /MP42C_MP42C_L1_R1.fastq.gz /MP42C_MP42C_L1_R2.fastq.gz NA ERR11518469.fastq.gz ERR11518469_1.fastq.gz -MP4B MP4B_MP4B 1 4 PE Homo sapiens (modern human) double half /MP4B_MP4B_L1_R1.fastq.gz /MP4B_MP4B_L1_R2.fastq.gz NA ERR11518478.fastq.gz ERR11518478_1.fastq.gz -MP51 MP51_MP51 1 4 PE Homo sapiens (modern human) double half /MP51_MP51_L1_R1.fastq.gz /MP51_MP51_L1_R2.fastq.gz NA ERR11518493.fastq.gz ERR11518493_1.fastq.gz -MP71 MP71_MP71 1 4 PE Homo sapiens (modern human) double half /MP71_MP71_L1_R1.fastq.gz /MP71_MP71_L1_R2.fastq.gz NA ERR11518498.fastq.gz ERR11518498_1.fastq.gz -MP77A MP77A_MP77A 1 4 PE Homo sapiens (modern human) double half /MP77A_MP77A_L1_R1.fastq.gz /MP77A_MP77A_L1_R2.fastq.gz NA ERR11518500.fastq.gz ERR11518500_1.fastq.gz -MP82 MP82_MP82 1 4 PE Homo sapiens (modern human) double half /MP82_MP82_L1_R1.fastq.gz /MP82_MP82_L1_R2.fastq.gz NA ERR11518502.fastq.gz ERR11518502_1.fastq.gz -MP80 MP80_MP80 1 4 PE Homo sapiens (modern human) double half /MP80_MP80_L1_R1.fastq.gz /MP80_MP80_L1_R2.fastq.gz NA ERR11518503.fastq.gz ERR11518503_1.fastq.gz -MP84C MP84C_MP84C 1 4 PE Homo sapiens (modern human) double half /MP84C_MP84C_L1_R1.fastq.gz /MP84C_MP84C_L1_R2.fastq.gz NA ERR11518512.fastq.gz ERR11518512_1.fastq.gz +MP42C MP42C_MP42C 1 4 SE Homo sapiens (modern human) double half /MP42C_MP42C_L1_R1.fastq.gz NA NA ERR11518469.fastq.gz NA +MP4B MP4B_MP4B 1 4 SE Homo sapiens (modern human) double half /MP4B_MP4B_L1_R1.fastq.gz NA NA ERR11518478.fastq.gz NA +MP51 MP51_MP51 1 4 SE Homo sapiens (modern human) double half /MP51_MP51_L1_R1.fastq.gz NA NA ERR11518493.fastq.gz NA +MP71 MP71_MP71 1 4 SE Homo sapiens (modern human) double half /MP71_MP71_L1_R1.fastq.gz NA NA ERR11518498.fastq.gz NA +MP77A MP77A_MP77A 1 4 SE Homo sapiens (modern human) double half /MP77A_MP77A_L1_R1.fastq.gz NA NA ERR11518500.fastq.gz NA +MP82 MP82_MP82 1 4 SE Homo sapiens (modern human) double half /MP82_MP82_L1_R1.fastq.gz NA NA ERR11518502.fastq.gz NA +MP80 MP80_MP80 1 4 SE Homo sapiens (modern human) double half /MP80_MP80_L1_R1.fastq.gz NA NA ERR11518503.fastq.gz NA +MP84C MP84C_MP84C 1 4 SE Homo sapiens (modern human) double half /MP84C_MP84C_L1_R1.fastq.gz NA NA ERR11518512.fastq.gz NA OTT-1160 OTT-1160_OTT-1160 1 4 SE Homo sapiens (modern human) double half /OTT-1160_OTT-1160_L1_R1.fastq.gz NA NA ERR11518538.fastq.gz NA OTT-1165 OTT-1165_OTT-1165 1 4 SE Homo sapiens (modern human) double half /OTT-1165_OTT-1165_L1_R1.fastq.gz NA NA ERR11518543.fastq.gz NA -MP63 MP63_MP63 1 4 PE Homo sapiens (modern human) double half /MP63_MP63_L1_R1.fastq.gz /MP63_MP63_L1_R2.fastq.gz NA ERR11518550.fastq.gz ERR11518550_1.fastq.gz +MP63 MP63_MP63 1 4 SE Homo sapiens (modern human) double half /MP63_MP63_L1_R1.fastq.gz NA NA ERR11518550.fastq.gz NA OTT-1174 OTT-1174_OTT-1174 1 4 SE Homo sapiens (modern human) double half /OTT-1174_OTT-1174_L1_R1.fastq.gz NA NA ERR11518552.fastq.gz NA QKI-4 QKI-4_QKI-4 1 4 SE Homo sapiens (modern human) double half /QKI-4_QKI-4_L1_R1.fastq.gz NA NA ERR11518562.fastq.gz NA OTT-1187 OTT-1187_OTT-1187 1 4 SE Homo sapiens (modern human) double half /OTT-1187_OTT-1187_L1_R1.fastq.gz NA NA ERR11518565.fastq.gz NA @@ -54,4 +54,4 @@ SHN-212 SHN-212_SHN-212 1 4 SE Homo sapiens (modern human) double half /SHN-355_SHN-355_L1_R1.fastq.gz NA NA ERR11518578.fastq.gz NA SHN-492 SHN-492_SHN-492 1 4 SE Homo sapiens (modern human) double half /SHN-492_SHN-492_L1_R1.fastq.gz NA NA ERR11518582.fastq.gz NA SHN-902 SHN-902_SHN-902 1 4 SE Homo sapiens (modern human) double half /SHN-902_SHN-902_L1_R1.fastq.gz NA NA ERR11518584.fastq.gz NA -MP3a MP3a_MP3a 1 4 PE Homo sapiens (modern human) double half /MP3a_MP3a_L1_R1.fastq.gz /MP3a_MP3a_L1_R2.fastq.gz NA ERR11518632.fastq.gz ERR11518632_1.fastq.gz +MP3a MP3a_MP3a 1 4 SE Homo sapiens (modern human) double half /MP3a_MP3a_L1_R1.fastq.gz NA NA ERR11518632.fastq.gz NA diff --git a/packages/2023_Salazar_MachuPicchu/script_versions.txt b/packages/2023_Salazar_MachuPicchu/script_versions.txt index be6857b..7a83b10 100644 --- a/packages/2023_Salazar_MachuPicchu/script_versions.txt +++ b/packages/2023_Salazar_MachuPicchu/script_versions.txt @@ -1,2 +1,2 @@ create_eager_input.sh: 0.2.1dev -source_me.sh for initial TSV: 0.2.1dev +source_me.sh for initial TSV: 0.2.3dev From bb68e8c56b1b8bde84b9d8f301ec509815269862 Mon Sep 17 00:00:00 2001 From: "Thiseas C. Lamnidis" Date: Wed, 4 Sep 2024 15:21:49 +0200 Subject: [PATCH 11/12] Add qualitymax option to config for 2023_Salazar_MacchuPicchu package --- .../2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.config | 2 ++ 1 file changed, 2 insertions(+) diff --git a/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.config b/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.config index 7fe6a40..2d784e7 100644 --- a/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.config +++ b/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.config @@ -37,4 +37,6 @@ params { You can see the default values for parameters within poseidon-eager at: https://github.com/poseidon-framework/poseidon-eager/blob/main/conf/Minotaur.config */ + + qualitymax = 93 // The uploaded data is already collapsed, so the quality scored for PE data exceed the default max quality score of 41. } From 35e50d2170a0e97d6a431c78e9b59ce2ba8969eb Mon Sep 17 00:00:00 2001 From: "Thiseas C. Lamnidis" Date: Wed, 4 Sep 2024 15:25:17 +0200 Subject: [PATCH 12/12] Bump config version --- .../2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.config b/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.config index 2d784e7..f244b3b 100644 --- a/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.config +++ b/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.config @@ -1,6 +1,6 @@ // Keep track of config versions config_template_version='0.3.0dev' -package_config_version='0.3.0dev' +package_config_version='0.3.1' minotaur_config_base='https://raw.githubusercontent.com/poseidon-framework/poseidon-eager/main/conf' // This configuration file is designed to be a used with the nf-core/eager pipeline.