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Create index option and tests #1

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added tests
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aerijman committed Jun 28, 2024
commit 0d02ad4eab3fa8d1d094c6ed59d606ba644f5233
6 changes: 3 additions & 3 deletions modules/aligners.nf
Original file line number Diff line number Diff line change
@@ -2,7 +2,7 @@ process bowtie2_create_index {
tag {"creating index"}
conda "bioconda:bowtie2=2.5.3"
publishDir "reference_bowtie2_index/"
cpus 24
cpus 4

input:
path(genome_fasta)
@@ -20,7 +20,7 @@ process bowtie2_create_index {
}

process bowtie2_align {
cpus 8
cpus 4
tag {library}
conda "bioconda:bowtie2=2.5.3 bioconda:samtools=1.19.2"
publishDir "${library}/"
@@ -48,7 +48,7 @@ process bowtie2_align {
}

process picard_MarkDuplicates{
cpus 8
cpus 4
tag {library}
conda "bioconda::picard=3.1.1"
publishDir "${library}/"
4 changes: 2 additions & 2 deletions modules/preprocessing.nf
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
process seqtk_sample {
cpus 8
cpus 4
tag {library}
conda "bioconda::seqtk=1.4"
publishDir "${library}/"
@@ -23,7 +23,7 @@ process seqtk_sample {
}

process fastp {
cpus 8
cpus 4
tag {library}
conda "bioconda::fastp=0.23.2"
publishDir "${library}/"
18 changes: 9 additions & 9 deletions modules/qc.nf
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
process samtools_flagstat{
cpus 8
cpus 4
tag {library}
conda "bioconda::samtools=1.15.1"
publishDir "${library}/"
@@ -20,7 +20,7 @@ process samtools_flagstat{


process picard_CollectGcBiasMetrics{
cpus 8
cpus 4
tag {library}
conda "bioconda::picard=3.1.1"
publishDir "${library}/"
@@ -46,7 +46,7 @@ process picard_CollectGcBiasMetrics{
}

process picard_CollectAlignmentSummaryMetrics{
cpus 8
cpus 4
tag {library}
conda "bioconda::picard=3.1.1"
publishDir "${library}/"
@@ -71,7 +71,7 @@ process picard_CollectAlignmentSummaryMetrics{
}

process picard_EstimateLibraryComplexity {
cpus 8
cpus 4
tag {library}
conda "bioconda::picard=3.1.1"
publishDir "${library}/"
@@ -96,7 +96,7 @@ process picard_EstimateLibraryComplexity {
}

process picard_CollectInsertSizeMetrics {
cpus 8
cpus 4
tag {library}
conda "bioconda::picard=3.1.1"
publishDir "${library}/"
@@ -125,7 +125,7 @@ process picard_CollectInsertSizeMetrics {
}

process fastqc {
cpus 8
cpus 4
tag {library}
conda "bioconda::fastqc=0.12.1"
publishDir "${library}/"
@@ -150,7 +150,7 @@ process fastqc {
}

process bedtools_genome_coverage {
cpus 8
cpus 4
tag {library}
conda "bioconda::bedtools=2.30"
publishDir "${library}/"
@@ -172,7 +172,7 @@ process bedtools_genome_coverage {
}

process multiqc {
cpus 8
cpus 4
tag {library}
conda "bioconda::multiqc=1.11"
publishDir "${library}/"
@@ -197,7 +197,7 @@ process multiqc {
}

process tasmanian {
cpus 8
cpus 1
tag {library}
conda "bioconda::tasmanian-mismatch=1.0.7 bioconda::samtools=1.13"
publishDir "${library}/"
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11 changes: 11 additions & 0 deletions test/run_tests.sh
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
gunzip small_ref.fa

# run tests and report
echo " test WITHOUT alignmnet index" > test_out.log
nextflow run ../main.nf --genome_fasta /mnt/home/aerijman/seqhimem02/FFPE_nextflow_workflow/test/small_ref.fa -with-conda -resume >> test_out.log 2>> test_out.log

echo "test WITH alignment index" >> test_out.log
nextflow run ../main.nf --genome_fasta /mnt/home/aerijman/seqhimem02/FFPE_nextflow_workflow/test/small_ref.fa \
--bowtie2_index /mnt/home/aerijman/seqhimem02/FFPE_nextflow_workflow/test/reference_bowtie2_index/ -with-conda -resume >> test_out.log 2>> test_out.log

rm -r reference_bowtie2_index/ r/ test_read/ work/
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716 changes: 716 additions & 0 deletions test/test_read.1.fastq

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716 changes: 716 additions & 0 deletions test/test_read.2.fastq

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