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https://github.com/MillironX/taxprofiler.git
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Merge pull request #42 from nf-core/refactor-adapterremoval
Refactor adapterremoval
This commit is contained in:
commit
b37a9c5576
4 changed files with 59 additions and 78 deletions
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@ -4,7 +4,7 @@
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"repos": {
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"repos": {
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"nf-core/modules": {
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"nf-core/modules": {
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"adapterremoval": {
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"adapterremoval": {
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"git_sha": "f0800157544a82ae222931764483331a81812012"
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"git_sha": "879d42c5e28661fe0a5e744c9e2c515868f9e08a"
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},
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},
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"cat/fastq": {
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"cat/fastq": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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42
modules/nf-core/modules/adapterremoval/main.nf
generated
42
modules/nf-core/modules/adapterremoval/main.nf
generated
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@ -12,14 +12,13 @@ process ADAPTERREMOVAL {
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path(adapterlist)
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path(adapterlist)
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output:
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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}.truncated.fastq.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}.discarded.fastq.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}.pair{1,2}.truncated.fastq.gz") , optional: true, emit: paired_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.fastq.gz") , optional: true, emit: collapsed
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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.fastq.gz") , optional: true, emit: collapsed_truncated
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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.fastq.gz") , optional: true, emit: paired_interleaved
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tuple val(meta), path("${prefix}.paired.gz") , optional: true, emit: paired_interleaved
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tuple val(meta), path('*.settings') , emit: settings
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tuple val(meta), path('*.log') , emit: log
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path "versions.yml" , emit: versions
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path "versions.yml" , emit: versions
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when:
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when:
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@ -38,10 +37,19 @@ process ADAPTERREMOVAL {
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$adapterlist \\
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$adapterlist \\
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--basename ${prefix} \\
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--basename ${prefix} \\
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--threads ${task.cpus} \\
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--threads ${task.cpus} \\
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--settings ${prefix}.log \\
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--seed 42 \\
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--seed 42 \\
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--gzip
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--gzip
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ensure_fastq() {
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if [ -f "\${1}" ]; then
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mv "\${1}" "\${1::-3}.fastq.gz"
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fi
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}
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ensure_fastq '${prefix}.truncated.gz'
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ensure_fastq '${prefix}.discarded.gz'
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cat <<-END_VERSIONS > versions.yml
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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"${task.process}":
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adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
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adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
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@ -56,10 +64,24 @@ process ADAPTERREMOVAL {
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$adapterlist \\
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$adapterlist \\
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--basename ${prefix} \\
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--basename ${prefix} \\
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--threads $task.cpus \\
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--threads $task.cpus \\
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--settings ${prefix}.log \\
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--seed 42 \\
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--seed 42 \\
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--gzip
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--gzip
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ensure_fastq() {
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if [ -f "\${1}" ]; then
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mv "\${1}" "\${1::-3}.fastq.gz"
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fi
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}
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ensure_fastq '${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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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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"${task.process}":
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adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
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adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
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14
modules/nf-core/modules/adapterremoval/meta.yml
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14
modules/nf-core/modules/adapterremoval/meta.yml
generated
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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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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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'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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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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- discarded:
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type: file
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type: file
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description: |
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description: |
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Adapter trimmed FastQ files of reads that did not pass filtering
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Adapter trimmed FastQ files of reads that did not pass filtering
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thresholds.
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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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- pair1_truncated:
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type: file
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type: file
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description: |
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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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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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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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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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- pair2_truncated:
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type: file
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type: file
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description: |
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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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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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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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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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- collapsed:
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type: file
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type: file
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description: |
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description: |
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Collapsed FastQ of paired-end reads that successfully merged with their
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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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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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- collapsed_truncated:
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type: file
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type: file
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description: |
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description: |
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Collapsed FastQ of paired-end reads that successfully merged with their
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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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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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- log:
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type: file
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type: file
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description: AdapterRemoval log 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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- versions:
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type: file
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type: file
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description: File containing software versions
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description: File containing software versions
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@ -5,11 +5,6 @@ Process short raw reads with AdapterRemoval
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include { ADAPTERREMOVAL as ADAPTERREMOVAL_SINGLE } from '../../modules/nf-core/modules/adapterremoval/main'
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include { ADAPTERREMOVAL as ADAPTERREMOVAL_SINGLE } from '../../modules/nf-core/modules/adapterremoval/main'
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include { ADAPTERREMOVAL as ADAPTERREMOVAL_PAIRED } from '../../modules/nf-core/modules/adapterremoval/main'
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include { ADAPTERREMOVAL as ADAPTERREMOVAL_PAIRED } from '../../modules/nf-core/modules/adapterremoval/main'
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include { CAT_FASTQ } from '../../modules/nf-core/modules/cat/fastq/main'
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include { CAT_FASTQ } from '../../modules/nf-core/modules/cat/fastq/main'
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include {
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ENSURE_FASTQ_EXTENSION as ENSURE_FASTQ_EXTENSION1;
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ENSURE_FASTQ_EXTENSION as ENSURE_FASTQ_EXTENSION2;
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ENSURE_FASTQ_EXTENSION as ENSURE_FASTQ_EXTENSION3;
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} from '../../modules/local/ensure_fastq_extension'
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workflow SHORTREAD_ADAPTERREMOVAL {
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workflow SHORTREAD_ADAPTERREMOVAL {
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@ -36,34 +31,27 @@ workflow SHORTREAD_ADAPTERREMOVAL {
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if ( params.shortread_clipmerge_mergepairs && !params.shortread_clipmerge_excludeunmerged ) {
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if ( params.shortread_clipmerge_mergepairs && !params.shortread_clipmerge_excludeunmerged ) {
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ENSURE_FASTQ_EXTENSION1(
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ch_concat_fastq = Channel.empty()
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Channel.empty().mix(
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.mix(
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ADAPTERREMOVAL_PAIRED.out.collapsed,
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ADAPTERREMOVAL_PAIRED.out.collapsed,
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ADAPTERREMOVAL_PAIRED.out.collapsed_truncated,
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ADAPTERREMOVAL_PAIRED.out.collapsed_truncated,
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ADAPTERREMOVAL_PAIRED.out.singles_truncated,
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ADAPTERREMOVAL_PAIRED.out.singles_truncated,
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ADAPTERREMOVAL_PAIRED.out.pair1_truncated,
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ADAPTERREMOVAL_PAIRED.out.paired_truncated
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ADAPTERREMOVAL_PAIRED.out.pair2_truncated
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)
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)
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.map { meta, reads ->
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meta.single_end = true
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[meta, reads]
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}
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)
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CAT_FASTQ(
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ENSURE_FASTQ_EXTENSION1.out.reads
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.groupTuple()
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.groupTuple()
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)
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// Paired-end reads cause a nested tuple during grouping.
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// We want to present a flat list of files to `CAT_FASTQ`.
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.map { meta, fastq -> [meta, fastq.flatten()] }
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ENSURE_FASTQ_EXTENSION2(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
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CAT_FASTQ(ch_concat_fastq)
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ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
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ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
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.mix(ENSURE_FASTQ_EXTENSION2.out.reads)
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.mix(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
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} else if ( params.shortread_clipmerge_mergepairs && params.shortread_clipmerge_excludeunmerged ) {
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} else if ( params.shortread_clipmerge_mergepairs && params.shortread_clipmerge_excludeunmerged ) {
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ENSURE_FASTQ_EXTENSION1(
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ch_concat_fastq = Channel.empty()
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Channel.empty().mix(
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.mix(
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ADAPTERREMOVAL_PAIRED.out.collapsed,
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ADAPTERREMOVAL_PAIRED.out.collapsed,
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ADAPTERREMOVAL_PAIRED.out.collapsed_truncated
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ADAPTERREMOVAL_PAIRED.out.collapsed_truncated
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)
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)
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@ -71,54 +59,25 @@ workflow SHORTREAD_ADAPTERREMOVAL {
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meta.single_end = true
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meta.single_end = true
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[meta, reads]
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[meta, reads]
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}
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}
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)
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CAT_FASTQ(
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ENSURE_FASTQ_EXTENSION1.out.reads
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.groupTuple()
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.groupTuple()
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)
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ENSURE_FASTQ_EXTENSION2(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
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CAT_FASTQ(ch_concat_fastq)
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ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
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ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
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.mix(ENSURE_FASTQ_EXTENSION2.out.reads)
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.mix(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
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} else {
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} else {
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ENSURE_FASTQ_EXTENSION1(
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ch_adapterremoval_reads_prepped = ADAPTERREMOVAL_PAIRED.out.paired_truncated
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ADAPTERREMOVAL_PAIRED.out.pair1_truncated
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.mix(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
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.map { meta, reads ->
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meta.single_end = true
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[meta, reads]
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}
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)
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ENSURE_FASTQ_EXTENSION2(
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ADAPTERREMOVAL_PAIRED.out.pair2_truncated
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.map { meta, reads ->
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meta.single_end = true
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[meta, reads]
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}
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)
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ENSURE_FASTQ_EXTENSION3(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
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ch_adapterremoval_reads_prepped = ENSURE_FASTQ_EXTENSION1.out.reads
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.join(ENSURE_FASTQ_EXTENSION2.out.reads)
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.groupTuple()
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.map { meta, pair1, pair2 ->
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meta.single_end = false
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[ meta, [ pair1, pair2 ].flatten() ]
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}
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.mix(ENSURE_FASTQ_EXTENSION3.out.reads)
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}
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}
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ch_versions = ch_versions.mix( ADAPTERREMOVAL_SINGLE.out.versions.first() )
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ch_versions = ch_versions.mix( ADAPTERREMOVAL_SINGLE.out.versions.first() )
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ch_versions = ch_versions.mix( ADAPTERREMOVAL_PAIRED.out.versions.first() )
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ch_versions = ch_versions.mix( ADAPTERREMOVAL_PAIRED.out.versions.first() )
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ch_multiqc_files = ch_multiqc_files.mix(
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ch_multiqc_files = ch_multiqc_files.mix(
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ADAPTERREMOVAL_PAIRED.out.log.collect{it[1]},
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ADAPTERREMOVAL_PAIRED.out.settings.collect{it[1]},
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ADAPTERREMOVAL_SINGLE.out.log.collect{it[1]}
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ADAPTERREMOVAL_SINGLE.out.settings.collect{it[1]}
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)
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)
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emit:
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emit:
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