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Fix: removes hardcoded flags and 'custom' file output for AdapterRemoval (#1357)
* fix: remove left-over unnecessary code * Removes hardcoded flags and more explicit output * Fix test md5
This commit is contained in:
James A. Fellows Yates
GitHub
parent
61c88c6233
commit
0816df1e8b
3 changed files with 77 additions and 28 deletions
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@ -11,9 +11,15 @@ process ADAPTERREMOVAL {
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path('*.fastq.gz'), emit: reads
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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('*.truncated.gz') , optional: true, emit: singles_truncated
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tuple val(meta), path('*.discarded.gz') , optional: true, emit: discarded
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tuple val(meta), path('*.pair1.truncated.gz') , optional: true, emit: pair1_truncated
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tuple val(meta), path('*.pair2.truncated.gz') , optional: true, emit: pair2_truncated
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tuple val(meta), path('*.collapsed.gz') , optional: true, emit: collapsed
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tuple val(meta), path('*.collapsed.truncated') , optional: true, emit: collapsed_truncated
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tuple val(meta), path('*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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when:
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task.ext.when == null || task.ext.when
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@ -28,30 +34,27 @@ process ADAPTERREMOVAL {
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--file1 $reads \\
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$args \\
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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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--output1 ${prefix}.trimmed.fastq.gz \\
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--seed 42 \\
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--gzip \\
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--gzip
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
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END_VERSIONS
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"""
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} else if (!meta.single_end && !meta.collapse) {
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} else if (!meta.single_end ) {
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"""
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AdapterRemoval \\
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--file1 ${reads[0]} \\
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--file2 ${reads[1]} \\
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$args \\
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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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--output1 ${prefix}.pair1.trimmed.fastq.gz \\
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--output2 ${prefix}.pair2.trimmed.fastq.gz \\
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--seed 42 \\
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--gzip \\
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--gzip
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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@ -63,13 +66,12 @@ process ADAPTERREMOVAL {
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AdapterRemoval \\
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--file1 ${reads[0]} \\
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--file2 ${reads[1]} \\
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--collapse \\
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$args \\
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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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--gzip
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cat *.collapsed.gz *.collapsed.truncated.gz > ${prefix}.merged.fastq.gz
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cat <<-END_VERSIONS > versions.yml
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@ -17,13 +17,13 @@ input:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false, collapse:false ]
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e.g. [ id:'test', single_end:false ]
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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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pattern: "*.{fq,fastq,fg.gz,fastq.gz}"
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pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
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output:
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- meta:
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@ -31,12 +31,45 @@ output:
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- reads:
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- singles_truncated:
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type: file
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description: |
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List of input adapter trimmed FastQ files of size 1 or 2 for
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single-end or collapsed data and paired-end data, respectively.
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pattern: "*.{fastq.gz}"
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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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- 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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- 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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- 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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- 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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- 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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- log:
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type: file
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description: AdapterRemoval log file
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@ -48,3 +81,4 @@ output:
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authors:
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- "@maxibor"
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- "@jfy133"
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@ -1,31 +1,44 @@
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- name: adapterremoval test_adapterremoval_single_end
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command: nextflow run ./tests/modules/adapterremoval -entry test_adapterremoval_single_end -c ./tests/config/nextflow.config -c ./tests/modules/adapterremoval/nextflow.config
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command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_single_end -c tests/config/nextflow.config
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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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md5sum: 2fd3d5d703b63ba33a83021fccf25f77
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- path: output/adapterremoval/test.trimmed.fastq.gz
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- path: output/adapterremoval/test.truncated.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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- name: adapterremoval test_adapterremoval_paired_end
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command: nextflow run ./tests/modules/adapterremoval -entry test_adapterremoval_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/adapterremoval/nextflow.config
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command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_paired_end -c tests/config/nextflow.config
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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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md5sum: b8a451d3981b327f3fdb44f40ba2d6d1
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- path: output/adapterremoval/test.pair1.trimmed.fastq.gz
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- path: output/adapterremoval/test.pair1.truncated.gz
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md5sum: 294a6277f0139bd597e57c6fa31f39c7
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- path: output/adapterremoval/test.pair2.trimmed.fastq.gz
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- path: output/adapterremoval/test.pair2.truncated.gz
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md5sum: de7b38e2c881bced8671acb1ab452d78
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- path: output/adapterremoval/test.singleton.truncated.gz
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- path: output/adapterremoval/versions.yml
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md5sum: fa621c887897da5a379c719399c17db7
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- name: adapterremoval test_adapterremoval_paired_end_collapse
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command: nextflow run ./tests/modules/adapterremoval -entry test_adapterremoval_paired_end_collapse -c ./tests/config/nextflow.config -c ./tests/modules/adapterremoval/nextflow.config
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command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_paired_end_collapse -c tests/config/nextflow.config
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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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md5sum: 7f0b2328152226e46101a535cce718b3
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- path: output/adapterremoval/test.merged.fastq.gz
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md5sum: 07a8f725bfd3ecbeabdc41b32d898dee
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md5sum: b8a451d3981b327f3fdb44f40ba2d6d1
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- path: output/adapterremoval/test.pair1.truncated.gz
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md5sum: 294a6277f0139bd597e57c6fa31f39c7
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- path: output/adapterremoval/test.pair2.truncated.gz
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md5sum: de7b38e2c881bced8671acb1ab452d78
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- path: output/adapterremoval/test.singleton.truncated.gz
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- path: output/adapterremoval/versions.yml
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md5sum: fd428f92a8446e0b34c5ae1c447215b8
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