diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index 1e2856c1..6704652c 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -15,6 +15,9 @@ nextflow_workflow { test("Parameters: default") { when { + params { + outdir = "$outputDir" + } workflow { """ input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") @@ -23,29 +26,9 @@ nextflow_workflow { } then { - assert workflow.success - assertAll( - { - with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"'] - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768" - } - } + { assert workflow.success}, + { assert snapshot(workflow.out).match() } ) } } diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap new file mode 100644 index 00000000..17beee5d --- /dev/null +++ b/workflows/sra/tests/main.nf.test.snap @@ -0,0 +1,281 @@ +{ + "Parameters: default": { + "content": [ + { + "0": [ + "samplesheet.csv:md5,636ddfb5fcd882e17303628f80df98d8" + ], + "1": [ + "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3" + ], + "2": [ + "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768" + ], + "3": [ + { + "base_count": "194930", + "experiment_accession": "DRX026011", + "experiment_alias": "DRX026011", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405", + "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d", + "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_bytes": "60275;61610", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30", + "id": "DRX026011_DRR028935", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "PAIRED", + "library_name": "day0_BbSQE-I", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cc01df82a9354bb6b3be93483b20c35a", + "md5_2": "941c9998d746416dad53c94c480ddf30", + "read_count": "965", + "run_accession": "DRR028935", + "run_alias": "DRR028935", + "sample_accession": "SAMD00024405", + "sample_alias": "SAMD00024405", + "sample_description": "Liquid culture", + "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium", + "scientific_name": "Botryococcus braunii Showa", + "secondary_sample_accession": "DRS019431", + "secondary_study_accession": "DRP002616", + "single_end": false, + "study_accession": "PRJDB3420", + "study_alias": "DRP002616", + "study_title": "Liquid culture of Botryococcus braunii, race B, Showa", + "submission_accession": "DRA002949", + "tax_id": "1202541" + }, + { + "base_count": "1996273", + "experiment_accession": "SRX6725035", + "experiment_alias": "Emb289P1_bin131", + "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus", + "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_bytes": "605358", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_md5": "0b512d2dc31685983456bd56fd836544", + "id": "SRX6725035_SRR9984183", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "Emb289P1_bin131", + "library_selection": "RANDOM", + "library_source": "METAGENOMIC", + "library_strategy": "WGS", + "md5_1": "0b512d2dc31685983456bd56fd836544", + "md5_2": "", + "read_count": "58", + "run_accession": "SRR9984183", + "run_alias": "Emb289P1_bin131.fastq", + "sample_accession": "SAMN12581720", + "sample_alias": "Emb289P1_bin131", + "sample_description": "Keywords: GSC:MIxS MIMAG:5.0", + "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium", + "scientific_name": "Defluviitaleaceae bacterium", + "secondary_sample_accession": "SRS5277011", + "secondary_study_accession": "SRP218535", + "single_end": true, + "study_accession": "PRJNA560329", + "study_alias": "PRJNA560329", + "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites", + "submission_accession": "SRA942061", + "tax_id": "2660712" + }, + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + } + ], + "4": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,c19fc0f920e57875881761cc944a46d7" + ], + "mappings": [ + "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3" + ], + "sample_mappings": [ + "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768" + ], + "samplesheet": [ + "samplesheet.csv:md5,636ddfb5fcd882e17303628f80df98d8" + ], + "sra_metadata": [ + { + "base_count": "194930", + "experiment_accession": "DRX026011", + "experiment_alias": "DRX026011", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405", + "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d", + "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_bytes": "60275;61610", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30", + "id": "DRX026011_DRR028935", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "PAIRED", + "library_name": "day0_BbSQE-I", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cc01df82a9354bb6b3be93483b20c35a", + "md5_2": "941c9998d746416dad53c94c480ddf30", + "read_count": "965", + "run_accession": "DRR028935", + "run_alias": "DRR028935", + "sample_accession": "SAMD00024405", + "sample_alias": "SAMD00024405", + "sample_description": "Liquid culture", + "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium", + "scientific_name": "Botryococcus braunii Showa", + "secondary_sample_accession": "DRS019431", + "secondary_study_accession": "DRP002616", + "single_end": false, + "study_accession": "PRJDB3420", + "study_alias": "DRP002616", + "study_title": "Liquid culture of Botryococcus braunii, race B, Showa", + "submission_accession": "DRA002949", + "tax_id": "1202541" + }, + { + "base_count": "1996273", + "experiment_accession": "SRX6725035", + "experiment_alias": "Emb289P1_bin131", + "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus", + "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_bytes": "605358", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_md5": "0b512d2dc31685983456bd56fd836544", + "id": "SRX6725035_SRR9984183", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "Emb289P1_bin131", + "library_selection": "RANDOM", + "library_source": "METAGENOMIC", + "library_strategy": "WGS", + "md5_1": "0b512d2dc31685983456bd56fd836544", + "md5_2": "", + "read_count": "58", + "run_accession": "SRR9984183", + "run_alias": "Emb289P1_bin131.fastq", + "sample_accession": "SAMN12581720", + "sample_alias": "Emb289P1_bin131", + "sample_description": "Keywords: GSC:MIxS MIMAG:5.0", + "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium", + "scientific_name": "Defluviitaleaceae bacterium", + "secondary_sample_accession": "SRS5277011", + "secondary_study_accession": "SRP218535", + "single_end": true, + "study_accession": "PRJNA560329", + "study_alias": "PRJNA560329", + "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites", + "submission_accession": "SRA942061", + "tax_id": "2660712" + }, + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + } + ], + "versions": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,c19fc0f920e57875881761cc944a46d7" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.2" + }, + "timestamp": "2024-10-15T12:58:48.512328" + } +} \ No newline at end of file diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test index c8d17876..1aa68be2 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -15,42 +15,23 @@ nextflow_workflow { test("Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...") { when { + params { + outdir = "$outputDir" + ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5" + nf_core_pipeline = "rnaseq" + sample_mapping_fields = "run_accession,library_layout" + } workflow { """ input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") """ } - params { - nf_core_pipeline = "rnaseq" - ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5" - sample_mapping_fields = "run_accession,library_layout" - } } then { - assert workflow.success - assertAll( - { - with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"strandedness"' , '"run_accession"'] - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('SINGLE') - } - }, - { - with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('SINGLE') - } - }, - { - with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "3b70bc9658eab4ba2f4ec98cb749ac9d" - } - } + { assert workflow.success}, + { assert snapshot(workflow.out).match() } ) } } diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap new file mode 100644 index 00000000..b85b2dd4 --- /dev/null +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap @@ -0,0 +1,125 @@ +{ + "Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...": { + "content": [ + { + "0": [ + "samplesheet.csv:md5,5f79ecf678ce5af375cf8749b56da139" + ], + "1": [ + "id_mappings.csv:md5,7345715e7db0a160efb8dd3be9ce58ac" + ], + "2": [ + "multiqc_config.yml:md5,3b70bc9658eab4ba2f4ec98cb749ac9d" + ], + "3": [ + { + "experiment_accession": "DRX026011", + "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d", + "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30", + "id": "DRX026011_DRR028935", + "library_layout": "PAIRED", + "md5_1": "cc01df82a9354bb6b3be93483b20c35a", + "md5_2": "941c9998d746416dad53c94c480ddf30", + "run_accession": "DRR028935", + "single_end": false + }, + { + "experiment_accession": "ERX1234253", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "library_layout": "SINGLE", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "run_accession": "ERR1160846", + "single_end": true + }, + { + "experiment_accession": "SRX6725035", + "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7", + "fastq_2": "", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_md5": "0b512d2dc31685983456bd56fd836544", + "id": "SRX6725035_SRR9984183", + "library_layout": "SINGLE", + "md5_1": "0b512d2dc31685983456bd56fd836544", + "md5_2": "", + "run_accession": "SRR9984183", + "single_end": true + } + ], + "4": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,c19fc0f920e57875881761cc944a46d7" + ], + "mappings": [ + "id_mappings.csv:md5,7345715e7db0a160efb8dd3be9ce58ac" + ], + "sample_mappings": [ + "multiqc_config.yml:md5,3b70bc9658eab4ba2f4ec98cb749ac9d" + ], + "samplesheet": [ + "samplesheet.csv:md5,5f79ecf678ce5af375cf8749b56da139" + ], + "sra_metadata": [ + { + "experiment_accession": "DRX026011", + "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d", + "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30", + "id": "DRX026011_DRR028935", + "library_layout": "PAIRED", + "md5_1": "cc01df82a9354bb6b3be93483b20c35a", + "md5_2": "941c9998d746416dad53c94c480ddf30", + "run_accession": "DRR028935", + "single_end": false + }, + { + "experiment_accession": "ERX1234253", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "library_layout": "SINGLE", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "run_accession": "ERR1160846", + "single_end": true + }, + { + "experiment_accession": "SRX6725035", + "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7", + "fastq_2": "", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_md5": "0b512d2dc31685983456bd56fd836544", + "id": "SRX6725035_SRR9984183", + "library_layout": "SINGLE", + "md5_1": "0b512d2dc31685983456bd56fd836544", + "md5_2": "", + "run_accession": "SRR9984183", + "single_end": true + } + ], + "versions": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,c19fc0f920e57875881761cc944a46d7" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.2" + }, + "timestamp": "2024-10-15T13:03:36.272997" + } +} \ No newline at end of file diff --git a/workflows/sra/tests/sra_download_method_aspera.nf.test b/workflows/sra/tests/sra_download_method_aspera.nf.test index d431a571..b6bc42af 100644 --- a/workflows/sra/tests/sra_download_method_aspera.nf.test +++ b/workflows/sra/tests/sra_download_method_aspera.nf.test @@ -15,40 +15,21 @@ nextflow_workflow { test("Parameters: --download_method aspera") { when { + params { + outdir = "$outputDir" + download_method = 'aspera' + } workflow { """ input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") """ } - params { - download_method = 'aspera' - } } then { - assert workflow.success - assertAll( - { - with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"'] - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768" - } - } + { assert workflow.success}, + { assert snapshot(workflow.out).match() } ) } } diff --git a/workflows/sra/tests/sra_download_method_aspera.nf.test.snap b/workflows/sra/tests/sra_download_method_aspera.nf.test.snap new file mode 100644 index 00000000..04a630a8 --- /dev/null +++ b/workflows/sra/tests/sra_download_method_aspera.nf.test.snap @@ -0,0 +1,281 @@ +{ + "Parameters: --download_method aspera": { + "content": [ + { + "0": [ + "samplesheet.csv:md5,d0f905867fa38eb136c88285669900c5" + ], + "1": [ + "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3" + ], + "2": [ + "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768" + ], + "3": [ + { + "base_count": "194930", + "experiment_accession": "DRX026011", + "experiment_alias": "DRX026011", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405", + "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d", + "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_bytes": "60275;61610", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30", + "id": "DRX026011_DRR028935", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "PAIRED", + "library_name": "day0_BbSQE-I", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cc01df82a9354bb6b3be93483b20c35a", + "md5_2": "941c9998d746416dad53c94c480ddf30", + "read_count": "965", + "run_accession": "DRR028935", + "run_alias": "DRR028935", + "sample_accession": "SAMD00024405", + "sample_alias": "SAMD00024405", + "sample_description": "Liquid culture", + "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium", + "scientific_name": "Botryococcus braunii Showa", + "secondary_sample_accession": "DRS019431", + "secondary_study_accession": "DRP002616", + "single_end": false, + "study_accession": "PRJDB3420", + "study_alias": "DRP002616", + "study_title": "Liquid culture of Botryococcus braunii, race B, Showa", + "submission_accession": "DRA002949", + "tax_id": "1202541" + }, + { + "base_count": "1996273", + "experiment_accession": "SRX6725035", + "experiment_alias": "Emb289P1_bin131", + "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus", + "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_bytes": "605358", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_md5": "0b512d2dc31685983456bd56fd836544", + "id": "SRX6725035_SRR9984183", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "Emb289P1_bin131", + "library_selection": "RANDOM", + "library_source": "METAGENOMIC", + "library_strategy": "WGS", + "md5_1": "0b512d2dc31685983456bd56fd836544", + "md5_2": "", + "read_count": "58", + "run_accession": "SRR9984183", + "run_alias": "Emb289P1_bin131.fastq", + "sample_accession": "SAMN12581720", + "sample_alias": "Emb289P1_bin131", + "sample_description": "Keywords: GSC:MIxS MIMAG:5.0", + "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium", + "scientific_name": "Defluviitaleaceae bacterium", + "secondary_sample_accession": "SRS5277011", + "secondary_study_accession": "SRP218535", + "single_end": true, + "study_accession": "PRJNA560329", + "study_alias": "PRJNA560329", + "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites", + "submission_accession": "SRA942061", + "tax_id": "2660712" + }, + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + } + ], + "4": [ + "versions.yml:md5,0aae1b802eabfe94891bf2d0fd0ddf60", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" + ], + "mappings": [ + "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3" + ], + "sample_mappings": [ + "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768" + ], + "samplesheet": [ + "samplesheet.csv:md5,d0f905867fa38eb136c88285669900c5" + ], + "sra_metadata": [ + { + "base_count": "194930", + "experiment_accession": "DRX026011", + "experiment_alias": "DRX026011", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405", + "fastq_1": 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"Emb289P1_bin131", + "sample_description": "Keywords: GSC:MIxS MIMAG:5.0", + "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium", + "scientific_name": "Defluviitaleaceae bacterium", + "secondary_sample_accession": "SRS5277011", + "secondary_study_accession": "SRP218535", + "single_end": true, + "study_accession": "PRJNA560329", + "study_alias": "PRJNA560329", + "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites", + "submission_accession": "SRA942061", + "tax_id": "2660712" + }, + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + } + ], + "versions": [ + "versions.yml:md5,0aae1b802eabfe94891bf2d0fd0ddf60", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.2" + }, + "timestamp": "2024-10-15T13:04:11.866017" + } +} \ No newline at end of file diff --git a/workflows/sra/tests/sra_download_method_sratools.nf.test b/workflows/sra/tests/sra_download_method_sratools.nf.test index e4f8c2d2..33e048a5 100644 --- a/workflows/sra/tests/sra_download_method_sratools.nf.test +++ b/workflows/sra/tests/sra_download_method_sratools.nf.test @@ -15,40 +15,21 @@ nextflow_workflow { test("Parameters: --download_method sratools") { when { + params { + outdir = "$outputDir" + download_method = 'sratools' + } workflow { """ input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") """ } - params { - download_method = 'sratools' - } } then { - assert workflow.success - assertAll( - { - with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"'] - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768" - } - } + { assert workflow.success}, + { assert snapshot(workflow.out).match() } ) } } diff --git a/workflows/sra/tests/sra_download_method_sratools.nf.test.snap b/workflows/sra/tests/sra_download_method_sratools.nf.test.snap new file mode 100644 index 00000000..2203c2e0 --- /dev/null +++ b/workflows/sra/tests/sra_download_method_sratools.nf.test.snap @@ -0,0 +1,281 @@ +{ + "Parameters: --download_method sratools": { + "content": [ + { + "0": [ + "samplesheet.csv:md5,1dc8ec98b2cc2d9f07ebd0f033c5e4eb" + ], + "1": [ + "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3" + ], + "2": [ + "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768" + ], + "3": [ + { + "base_count": "194930", + "experiment_accession": "DRX026011", + "experiment_alias": "DRX026011", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405", + "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,1c3a691ea99767f25de2492440a02cb7", + "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,6fa02d3e52613cfe3464cc7a29f227d4", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_bytes": "60275;61610", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30", + "id": "DRX026011_DRR028935", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "PAIRED", + "library_name": "day0_BbSQE-I", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cc01df82a9354bb6b3be93483b20c35a", + "md5_2": "941c9998d746416dad53c94c480ddf30", + "read_count": "965", + "run_accession": "DRR028935", + "run_alias": "DRR028935", + "sample_accession": "SAMD00024405", + "sample_alias": "SAMD00024405", + "sample_description": "Liquid culture", + "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium", + "scientific_name": "Botryococcus braunii Showa", + "secondary_sample_accession": "DRS019431", + "secondary_study_accession": "DRP002616", + "single_end": false, + "study_accession": "PRJDB3420", + "study_alias": "DRP002616", + "study_title": "Liquid culture of Botryococcus braunii, race B, Showa", + "submission_accession": "DRA002949", + "tax_id": "1202541" + }, + { + "base_count": "1996273", + "experiment_accession": "SRX6725035", + "experiment_alias": "Emb289P1_bin131", + "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus", + "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,aadf8ac0a6a3282b52404aa4dd14497c", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_bytes": "605358", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_md5": "0b512d2dc31685983456bd56fd836544", + "id": "SRX6725035_SRR9984183", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "Emb289P1_bin131", + "library_selection": "RANDOM", + "library_source": "METAGENOMIC", + "library_strategy": "WGS", + "md5_1": "0b512d2dc31685983456bd56fd836544", + "md5_2": "", + "read_count": "58", + "run_accession": "SRR9984183", + "run_alias": "Emb289P1_bin131.fastq", + "sample_accession": "SAMN12581720", + "sample_alias": "Emb289P1_bin131", + "sample_description": "Keywords: GSC:MIxS MIMAG:5.0", + "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium", + "scientific_name": "Defluviitaleaceae bacterium", + "secondary_sample_accession": "SRS5277011", + "secondary_study_accession": "SRP218535", + "single_end": true, + "study_accession": "PRJNA560329", + "study_alias": "PRJNA560329", + "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites", + "submission_accession": "SRA942061", + "tax_id": "2660712" + }, + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,98515d664854f1c96f55ac836fb671b9", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + } + ], + "4": [ + "versions.yml:md5,0bb049f166e93b3d9866ed7e4407c6c9", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" + ], + "mappings": [ + "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3" + ], + "sample_mappings": [ + "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768" + ], + "samplesheet": [ + "samplesheet.csv:md5,1dc8ec98b2cc2d9f07ebd0f033c5e4eb" + ], + "sra_metadata": [ + { + "base_count": "194930", + "experiment_accession": "DRX026011", + "experiment_alias": "DRX026011", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405", + "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,1c3a691ea99767f25de2492440a02cb7", + "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,6fa02d3e52613cfe3464cc7a29f227d4", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_bytes": "60275;61610", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30", + "id": "DRX026011_DRR028935", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "PAIRED", + "library_name": "day0_BbSQE-I", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cc01df82a9354bb6b3be93483b20c35a", + "md5_2": "941c9998d746416dad53c94c480ddf30", + "read_count": "965", + "run_accession": "DRR028935", + "run_alias": "DRR028935", + "sample_accession": "SAMD00024405", + "sample_alias": "SAMD00024405", + "sample_description": "Liquid culture", + "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium", + "scientific_name": "Botryococcus braunii Showa", + "secondary_sample_accession": "DRS019431", + "secondary_study_accession": "DRP002616", + "single_end": false, + "study_accession": "PRJDB3420", + "study_alias": "DRP002616", + "study_title": "Liquid culture of Botryococcus braunii, race B, Showa", + "submission_accession": "DRA002949", + "tax_id": "1202541" + }, + { + "base_count": "1996273", + "experiment_accession": "SRX6725035", + "experiment_alias": "Emb289P1_bin131", + "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus", + "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,aadf8ac0a6a3282b52404aa4dd14497c", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_bytes": "605358", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_md5": "0b512d2dc31685983456bd56fd836544", + "id": "SRX6725035_SRR9984183", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "Emb289P1_bin131", + "library_selection": "RANDOM", + "library_source": "METAGENOMIC", + "library_strategy": "WGS", + "md5_1": "0b512d2dc31685983456bd56fd836544", + "md5_2": "", + "read_count": "58", + "run_accession": "SRR9984183", + "run_alias": "Emb289P1_bin131.fastq", + "sample_accession": "SAMN12581720", + "sample_alias": "Emb289P1_bin131", + "sample_description": "Keywords: GSC:MIxS MIMAG:5.0", + "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium", + "scientific_name": "Defluviitaleaceae bacterium", + "secondary_sample_accession": "SRS5277011", + "secondary_study_accession": "SRP218535", + "single_end": true, + "study_accession": "PRJNA560329", + "study_alias": "PRJNA560329", + "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites", + "submission_accession": "SRA942061", + "tax_id": "2660712" + }, + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,98515d664854f1c96f55ac836fb671b9", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + } + ], + "versions": [ + "versions.yml:md5,0bb049f166e93b3d9866ed7e4407c6c9", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.2" + }, + "timestamp": "2024-10-15T13:04:40.461589" + } +} \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test index 72f8d595..886aef19 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -15,40 +15,21 @@ nextflow_workflow { test("Parameters: --nf_core_pipeline atacseq") { when { + params { + outdir = "$outputDir" + nf_core_pipeline = "atacseq" + } workflow { """ input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") """ } - params { - nf_core_pipeline = "atacseq" - } } then { - assert workflow.success - assertAll( - { - with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"replicate"', '"run_accession"'] - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768" - } - } + { assert workflow.success}, + { assert snapshot(workflow.out).match() } ) } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap new file mode 100644 index 00000000..12c26342 --- /dev/null +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap @@ -0,0 +1,281 @@ +{ + "Parameters: --nf_core_pipeline atacseq": { + "content": [ + { + "0": [ + "samplesheet.csv:md5,ec54a949c41851e8c5c20dc595992d25" + ], + "1": [ + "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3" + ], + "2": [ + "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768" + ], + "3": [ + { + "base_count": "194930", + "experiment_accession": "DRX026011", + "experiment_alias": "DRX026011", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405", + "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d", + "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_bytes": "60275;61610", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30", + "id": "DRX026011_DRR028935", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "PAIRED", + "library_name": "day0_BbSQE-I", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cc01df82a9354bb6b3be93483b20c35a", + "md5_2": "941c9998d746416dad53c94c480ddf30", + "read_count": "965", + "run_accession": "DRR028935", + "run_alias": "DRR028935", + "sample_accession": "SAMD00024405", + "sample_alias": "SAMD00024405", + "sample_description": "Liquid culture", + "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium", + "scientific_name": "Botryococcus braunii Showa", + "secondary_sample_accession": "DRS019431", + "secondary_study_accession": "DRP002616", + "single_end": false, + "study_accession": "PRJDB3420", + "study_alias": "DRP002616", + "study_title": "Liquid culture of Botryococcus braunii, race B, Showa", + "submission_accession": "DRA002949", + "tax_id": "1202541" + }, + { + "base_count": "1996273", + "experiment_accession": "SRX6725035", + "experiment_alias": "Emb289P1_bin131", + "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus", + "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_bytes": "605358", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_md5": "0b512d2dc31685983456bd56fd836544", + "id": "SRX6725035_SRR9984183", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "Emb289P1_bin131", + "library_selection": "RANDOM", + "library_source": "METAGENOMIC", + "library_strategy": "WGS", + "md5_1": "0b512d2dc31685983456bd56fd836544", + "md5_2": "", + "read_count": "58", + "run_accession": "SRR9984183", + "run_alias": "Emb289P1_bin131.fastq", + "sample_accession": "SAMN12581720", + "sample_alias": "Emb289P1_bin131", + "sample_description": "Keywords: GSC:MIxS MIMAG:5.0", + "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium", + "scientific_name": "Defluviitaleaceae bacterium", + "secondary_sample_accession": "SRS5277011", + "secondary_study_accession": "SRP218535", + "single_end": true, + "study_accession": "PRJNA560329", + "study_alias": "PRJNA560329", + "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites", + "submission_accession": "SRA942061", + "tax_id": "2660712" + }, + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + } + ], + "4": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,c19fc0f920e57875881761cc944a46d7" + ], + "mappings": [ + "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3" + ], + "sample_mappings": [ + "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768" + ], + "samplesheet": [ + "samplesheet.csv:md5,ec54a949c41851e8c5c20dc595992d25" + ], + "sra_metadata": [ + { + "base_count": "194930", + "experiment_accession": "DRX026011", + "experiment_alias": "DRX026011", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405", + "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d", + "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_bytes": "60275;61610", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30", + "id": "DRX026011_DRR028935", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "PAIRED", + "library_name": "day0_BbSQE-I", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cc01df82a9354bb6b3be93483b20c35a", + "md5_2": "941c9998d746416dad53c94c480ddf30", + "read_count": "965", + "run_accession": "DRR028935", + "run_alias": "DRR028935", + "sample_accession": "SAMD00024405", + "sample_alias": "SAMD00024405", + "sample_description": "Liquid culture", + "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium", + "scientific_name": "Botryococcus braunii Showa", + "secondary_sample_accession": "DRS019431", + "secondary_study_accession": "DRP002616", + "single_end": false, + "study_accession": "PRJDB3420", + "study_alias": "DRP002616", + "study_title": "Liquid culture of Botryococcus braunii, race B, Showa", + "submission_accession": "DRA002949", + "tax_id": "1202541" + }, + { + "base_count": "1996273", + "experiment_accession": "SRX6725035", + "experiment_alias": "Emb289P1_bin131", + "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus", + "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_bytes": "605358", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_md5": "0b512d2dc31685983456bd56fd836544", + "id": "SRX6725035_SRR9984183", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "Emb289P1_bin131", + "library_selection": "RANDOM", + "library_source": "METAGENOMIC", + "library_strategy": "WGS", + "md5_1": "0b512d2dc31685983456bd56fd836544", + "md5_2": "", + "read_count": "58", + "run_accession": "SRR9984183", + "run_alias": "Emb289P1_bin131.fastq", + "sample_accession": "SAMN12581720", + "sample_alias": "Emb289P1_bin131", + "sample_description": "Keywords: GSC:MIxS MIMAG:5.0", + "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium", + "scientific_name": "Defluviitaleaceae bacterium", + "secondary_sample_accession": "SRS5277011", + "secondary_study_accession": "SRP218535", + "single_end": true, + "study_accession": "PRJNA560329", + "study_alias": "PRJNA560329", + "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites", + "submission_accession": "SRA942061", + "tax_id": "2660712" + }, + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + } + ], + "versions": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,c19fc0f920e57875881761cc944a46d7" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.2" + }, + "timestamp": "2024-10-15T13:05:13.825847" + } +} \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test index 2e20902a..7f67aefb 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test @@ -15,40 +15,21 @@ nextflow_workflow { test("Parameters: --nf_core_pipeline rnaseq") { when { + params { + outdir = "$outputDir" + nf_core_pipeline = "rnaseq" + } workflow { """ input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") """ } - params { - nf_core_pipeline = "rnaseq" - } } then { - assert workflow.success - assertAll( - { - with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"strandedness"' , '"run_accession"'] - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768" - } - } + { assert workflow.success}, + { assert snapshot(workflow.out).match() } ) } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap new file mode 100644 index 00000000..61f6cd12 --- /dev/null +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap @@ -0,0 +1,281 @@ +{ + "Parameters: --nf_core_pipeline rnaseq": { + "content": [ + { + "0": [ + "samplesheet.csv:md5,633beb86dd3622ea86f5346425f8a574" + ], + "1": [ + "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3" + ], + "2": [ + "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768" + ], + "3": [ + { + "base_count": "194930", + "experiment_accession": "DRX026011", + "experiment_alias": "DRX026011", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405", + "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d", + "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_bytes": "60275;61610", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_galaxy": 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with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"fasta"', '"run_accession"'] - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768" - } - } + { assert workflow.success}, + { assert snapshot(workflow.out).match() } ) } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap new file mode 100644 index 00000000..d4d7047e --- /dev/null +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap @@ -0,0 +1,281 @@ +{ + "Parameters: --nf_core_pipeline taxprofiler": { + "content": [ + { + "0": [ + "samplesheet.csv:md5,790f0cad9d01e35e0d1e03f199851770" + ], + "1": [ + "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3" + ], + "2": [ + "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768" + ], + "3": [ + { + "base_count": "194930", + "experiment_accession": "DRX026011", + "experiment_alias": "DRX026011", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405", + "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d", + "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15", + "fastq_aspera": 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{ + params { + outdir = "$outputDir" + nf_core_pipeline = "viralrecon" + } workflow { """ input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") """ } - params { - nf_core_pipeline = "viralrecon" - } } then { - assert workflow.success - assertAll( - { - with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"'] - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768" - } - } + { assert workflow.success}, + { assert snapshot(workflow.out).match() } ) } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap new file mode 100644 index 00000000..a9b14b4d --- /dev/null +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap @@ -0,0 +1,281 @@ +{ + "Parameters: --nf_core_pipeline viralrecon": { + "content": [ + { + "0": [ + "samplesheet.csv:md5,d81fe6175afaa01183475a6e28c7caa9" + ], + "1": [ + "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3" + ], + "2": [ + "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768" + ], + "3": [ + { + "base_count": "194930", + "experiment_accession": "DRX026011", + "experiment_alias": "DRX026011", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405", + "fastq_1": 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a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -14,40 +14,21 @@ nextflow_workflow { test("Parameters: --skip_fastq_download") { when { + params { + outdir = "$outputDir" + skip_fastq_download = true + } workflow { """ input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") """ } - params { - skip_fastq_download = true - } } then { - assert workflow.success - assertAll( - { - with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"'] - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768" - } - } + { assert workflow.success}, + { assert snapshot(workflow.out).match() } ) } } diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap new file mode 100644 index 00000000..34ee72c1 --- /dev/null +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap @@ -0,0 +1,279 @@ +{ + "Parameters: --skip_fastq_download": { + "content": [ + { + "0": [ + "samplesheet.csv:md5,0788cf0fed166518e5d1399532f8068f" + ], + "1": [ + "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3" + ], + "2": [ + "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768" + ], + "3": [ + { + "base_count": "194930", + "experiment_accession": "DRX026011", + "experiment_alias": "DRX026011", + 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