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Refactor adapterremoval (#1491)
* refactor: insert .fastq file extensions * style: insert whitespace * refactor: create paired output * refactor: rename settings from log Requested by @jfy133 * tests: correct expected output * fix: remove settings option due to default * chore: rename output patterns * refactor: omit paired files in single-end * refactor: rename output to settings
This commit is contained in:
Moritz E. Beber
GitHub
parent
13cc32399c
commit
879d42c5e2
3 changed files with 53 additions and 31 deletions
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@ -12,15 +12,14 @@ process ADAPTERREMOVAL {
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path(adapterlist)
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output:
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tuple val(meta), path("${prefix}.truncated.gz") , optional: true, emit: singles_truncated
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tuple val(meta), path("${prefix}.discarded.gz") , optional: true, emit: discarded
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tuple val(meta), path("${prefix}.pair1.truncated.gz") , optional: true, emit: pair1_truncated
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tuple val(meta), path("${prefix}.pair2.truncated.gz") , optional: true, emit: pair2_truncated
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tuple val(meta), path("${prefix}.collapsed.gz") , optional: true, emit: collapsed
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tuple val(meta), path("${prefix}.collapsed.truncated.gz") , optional: true, emit: collapsed_truncated
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tuple val(meta), path("${prefix}.paired.gz") , optional: true, emit: paired_interleaved
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tuple val(meta), path('*.log') , emit: log
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path "versions.yml" , emit: versions
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tuple val(meta), path("${prefix}.truncated.fastq.gz") , optional: true, emit: singles_truncated
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tuple val(meta), path("${prefix}.discarded.fastq.gz") , optional: true, emit: discarded
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tuple val(meta), path("${prefix}.pair{1,2}.truncated.fastq.gz") , optional: true, emit: paired_truncated
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tuple val(meta), path("${prefix}.collapsed.fastq.gz") , optional: true, emit: collapsed
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tuple val(meta), path("${prefix}.collapsed.truncated.fastq.gz") , optional: true, emit: collapsed_truncated
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tuple val(meta), path("${prefix}.paired.fastq.gz") , optional: true, emit: paired_interleaved
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tuple val(meta), path('*.settings') , emit: settings
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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@ -38,10 +37,19 @@ process ADAPTERREMOVAL {
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$adapterlist \\
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--basename ${prefix} \\
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--threads ${task.cpus} \\
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--settings ${prefix}.log \\
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--seed 42 \\
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--gzip
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ensure_fastq() {
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if [ -f "\${1}" ]; then
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mv "\${1}" "\${1::-3}.fastq.gz"
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fi
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}
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ensure_fastq '${prefix}.truncated.gz'
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ensure_fastq '${prefix}.discarded.gz'
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
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@ -56,10 +64,24 @@ process ADAPTERREMOVAL {
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$adapterlist \\
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--basename ${prefix} \\
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--threads $task.cpus \\
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--settings ${prefix}.log \\
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--seed 42 \\
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--gzip
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ensure_fastq() {
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if [ -f "\${1}" ]; then
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mv "\${1}" "\${1::-3}.fastq.gz"
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fi
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}
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ensure_fastq '${prefix}.truncated.gz'
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ensure_fastq '${prefix}.discarded.gz'
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ensure_fastq '${prefix}.pair1.truncated.gz'
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ensure_fastq '${prefix}.pair2.truncated.gz'
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ensure_fastq '${prefix}.collapsed.gz'
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ensure_fastq '${prefix}.collapsed.truncated.gz'
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ensure_fastq '${prefix}.paired.gz'
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
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@ -43,43 +43,43 @@ output:
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Adapter trimmed FastQ files of either single-end reads, or singleton
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'orphaned' reads from merging of paired-end data (i.e., one of the pair
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was lost due to filtering thresholds).
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pattern: "*.truncated.gz"
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pattern: "*.truncated.fastq.gz"
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- discarded:
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type: file
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description: |
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Adapter trimmed FastQ files of reads that did not pass filtering
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thresholds.
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pattern: "*.discarded.gz"
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pattern: "*.discarded.fastq.gz"
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- pair1_truncated:
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type: file
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description: |
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Adapter trimmed R1 FastQ files of paired-end reads that did not merge
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with their respective R2 pair due to long templates. The respective pair
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is stored in 'pair2_truncated'.
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pattern: "*.pair1.truncated.gz"
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pattern: "*.pair1.truncated.fastq.gz"
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- pair2_truncated:
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type: file
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description: |
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Adapter trimmed R2 FastQ files of paired-end reads that did not merge
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with their respective R1 pair due to long templates. The respective pair
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is stored in 'pair1_truncated'.
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pattern: "*.pair2.truncated.gz"
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pattern: "*.pair2.truncated.fastq.gz"
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- collapsed:
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type: file
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description: |
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Collapsed FastQ of paired-end reads that successfully merged with their
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respective R1 pair but were not trimmed.
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pattern: "*.collapsed.gz"
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pattern: "*.collapsed.fastq.gz"
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- collapsed_truncated:
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type: file
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description: |
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Collapsed FastQ of paired-end reads that successfully merged with their
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respective R1 pair and were trimmed of adapter due to sufficient overlap.
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pattern: "*.collapsed.truncated.gz"
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pattern: "*.collapsed.truncated.fastq.gz"
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- log:
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type: file
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description: AdapterRemoval log file
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pattern: "*.log"
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pattern: "*.settings"
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- versions:
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type: file
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description: File containing software versions
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@ -3,10 +3,10 @@
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tags:
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- adapterremoval
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files:
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- path: output/adapterremoval/test.discarded.gz
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- path: output/adapterremoval/test.log
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- path: output/adapterremoval/test.discarded.fastq.gz
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- path: output/adapterremoval/test.settings
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md5sum: 2fd3d5d703b63ba33a83021fccf25f77
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- path: output/adapterremoval/test.truncated.gz
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- path: output/adapterremoval/test.truncated.fastq.gz
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md5sum: 62139afee94defad5b83bdd0b8475a1f
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- path: output/adapterremoval/versions.yml
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md5sum: ac5b46719719b7ee62739530b80869fc
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@ -16,12 +16,12 @@
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tags:
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- adapterremoval
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files:
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- path: output/adapterremoval/test.discarded.gz
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- path: output/adapterremoval/test.log
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- path: output/adapterremoval/test.discarded.fastq.gz
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- path: output/adapterremoval/test.settings
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md5sum: b8a451d3981b327f3fdb44f40ba2d6d1
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- path: output/adapterremoval/test.pair1.truncated.gz
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- path: output/adapterremoval/test.pair1.truncated.fastq.gz
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md5sum: 294a6277f0139bd597e57c6fa31f39c7
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- path: output/adapterremoval/test.pair2.truncated.gz
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- path: output/adapterremoval/test.pair2.truncated.fastq.gz
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md5sum: de7b38e2c881bced8671acb1ab452d78
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- path: output/adapterremoval/versions.yml
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md5sum: fa621c887897da5a379c719399c17db7
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@ -31,15 +31,15 @@
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tags:
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- adapterremoval
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files:
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- path: output/adapterremoval/test.collapsed.gz
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- path: output/adapterremoval/test.collapsed.fastq.gz
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md5sum: ff956de3532599a56c3efe5369f0953f
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- path: output/adapterremoval/test.collapsed.truncated.gz
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- path: output/adapterremoval/test.discarded.gz
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- path: output/adapterremoval/test.log
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- path: output/adapterremoval/test.collapsed.truncated.fastq.gz
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- path: output/adapterremoval/test.discarded.fastq.gz
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- path: output/adapterremoval/test.settings
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md5sum: 7f0b2328152226e46101a535cce718b3
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- path: output/adapterremoval/test.pair1.truncated.gz
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- path: output/adapterremoval/test.pair1.truncated.fastq.gz
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md5sum: 683be19bc1c83008944b6b719bfa34e1
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- path: output/adapterremoval/test.pair2.truncated.gz
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- path: output/adapterremoval/test.pair2.truncated.fastq.gz
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md5sum: e6548fe061f3ef86368b26da930174d0
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- path: output/adapterremoval/versions.yml
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md5sum: 78f589bb313c8da0147ca8ce77d7f3bf
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