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 2022-03-03 10:01:39 +01:00 committed by GitHub
parent 61c88c6233
commit 0816df1e8b
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3 changed files with 77 additions and 28 deletions

View file

@ -11,7 +11,13 @@ process ADAPTERREMOVAL {
tuple val(meta), path(reads)
output:
tuple val(meta), path('*.fastq.gz'), emit: reads
tuple val(meta), path('*.truncated.gz') , optional: true, emit: singles_truncated
tuple val(meta), path('*.discarded.gz') , optional: true, emit: discarded
tuple val(meta), path('*.pair1.truncated.gz') , optional: true, emit: pair1_truncated
tuple val(meta), path('*.pair2.truncated.gz') , optional: true, emit: pair2_truncated
tuple val(meta), path('*.collapsed.gz') , optional: true, emit: collapsed
tuple val(meta), path('*.collapsed.truncated') , optional: true, emit: collapsed_truncated
tuple val(meta), path('*paired.gz') , optional: true, emit: paired_interleaved
tuple val(meta), path('*.log') , emit: log
path "versions.yml" , emit: versions
@ -28,30 +34,27 @@ process ADAPTERREMOVAL {
--file1 $reads \\
$args \\
--basename $prefix \\
--threads $task.cpus \\
--threads ${task.cpus} \\
--settings ${prefix}.log \\
--output1 ${prefix}.trimmed.fastq.gz \\
--seed 42 \\
--gzip \\
--gzip
cat <<-END_VERSIONS > versions.yml
"${task.process}":
adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
END_VERSIONS
"""
} else if (!meta.single_end && !meta.collapse) {
} else if (!meta.single_end ) {
"""
AdapterRemoval \\
--file1 ${reads[0]} \\
--file2 ${reads[1]} \\
$args \\
--basename $prefix \\
--threads $task.cpus \\
--threads ${task.cpus} \\
--settings ${prefix}.log \\
--output1 ${prefix}.pair1.trimmed.fastq.gz \\
--output2 ${prefix}.pair2.trimmed.fastq.gz \\
--seed 42 \\
--gzip \\
--gzip
cat <<-END_VERSIONS > versions.yml
"${task.process}":
@ -63,13 +66,12 @@ process ADAPTERREMOVAL {
AdapterRemoval \\
--file1 ${reads[0]} \\
--file2 ${reads[1]} \\
--collapse \\
$args \\
--basename $prefix \\
--threads $task.cpus \\
--settings ${prefix}.log \\
--seed 42 \\
--gzip \\
--gzip
cat *.collapsed.gz *.collapsed.truncated.gz > ${prefix}.merged.fastq.gz
cat <<-END_VERSIONS > versions.yml

View file

@ -17,13 +17,13 @@ input:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false, collapse:false ]
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
pattern: "*.{fq,fastq,fg.gz,fastq.gz}"
pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
output:
- meta:
@ -31,12 +31,45 @@ output:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
- singles_truncated:
type: file
description: |
List of input adapter trimmed FastQ files of size 1 or 2 for
single-end or collapsed data and paired-end data, respectively.
pattern: "*.{fastq.gz}"
Adapter trimmed FastQ files of either single-end reads, or singleton
'orphaned' reads from merging of paired-end data (i.e., one of the pair
was lost due to filtering thresholds).
pattern: "*.truncated.gz"
- discarded:
type: file
description: |
Adapter trimmed FastQ files of reads that did not pass filtering
thresholds.
pattern: "*.discarded.gz"
- pair1_truncated:
type: file
description: |
Adapter trimmed R1 FastQ files of paired-end reads that did not merge
with their respective R2 pair due to long templates. The respective pair
is stored in 'pair2_truncated'.
pattern: "*.pair1.truncated.gz"
- pair2_truncated:
type: file
description: |
Adapter trimmed R2 FastQ files of paired-end reads that did not merge
with their respective R1 pair due to long templates. The respective pair
is stored in 'pair1_truncated'.
pattern: "*.pair2.truncated.gz"
- collapsed:
type: file
description: |
Collapsed FastQ of paired-end reads that successfully merged with their
respective R1 pair but were not trimmed.
pattern: "*.collapsed.gz"
- collapsed_truncated:
type: file
description: |
Collapsed FastQ of paired-end reads that successfully merged with their
respective R1 pair and were trimmed of adapter due to sufficient overlap.
pattern: "*.collapsed.truncated.gz"
- log:
type: file
description: AdapterRemoval log file
@ -48,3 +81,4 @@ output:
authors:
- "@maxibor"
- "@jfy133"

View file

@ -1,31 +1,44 @@
- name: adapterremoval test_adapterremoval_single_end
command: nextflow run ./tests/modules/adapterremoval -entry test_adapterremoval_single_end -c ./tests/config/nextflow.config -c ./tests/modules/adapterremoval/nextflow.config
command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_single_end -c tests/config/nextflow.config
tags:
- adapterremoval
files:
- path: output/adapterremoval/test.discarded.gz
- path: output/adapterremoval/test.log
md5sum: 2fd3d5d703b63ba33a83021fccf25f77
- path: output/adapterremoval/test.trimmed.fastq.gz
- path: output/adapterremoval/test.truncated.gz
md5sum: 62139afee94defad5b83bdd0b8475a1f
- path: output/adapterremoval/versions.yml
md5sum: ac5b46719719b7ee62739530b80869fc
- name: adapterremoval test_adapterremoval_paired_end
command: nextflow run ./tests/modules/adapterremoval -entry test_adapterremoval_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/adapterremoval/nextflow.config
command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_paired_end -c tests/config/nextflow.config
tags:
- adapterremoval
files:
- path: output/adapterremoval/test.discarded.gz
- path: output/adapterremoval/test.log
md5sum: b8a451d3981b327f3fdb44f40ba2d6d1
- path: output/adapterremoval/test.pair1.trimmed.fastq.gz
- path: output/adapterremoval/test.pair1.truncated.gz
md5sum: 294a6277f0139bd597e57c6fa31f39c7
- path: output/adapterremoval/test.pair2.trimmed.fastq.gz
- path: output/adapterremoval/test.pair2.truncated.gz
md5sum: de7b38e2c881bced8671acb1ab452d78
- path: output/adapterremoval/test.singleton.truncated.gz
- path: output/adapterremoval/versions.yml
md5sum: fa621c887897da5a379c719399c17db7
- name: adapterremoval test_adapterremoval_paired_end_collapse
command: nextflow run ./tests/modules/adapterremoval -entry test_adapterremoval_paired_end_collapse -c ./tests/config/nextflow.config -c ./tests/modules/adapterremoval/nextflow.config
command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_paired_end_collapse -c tests/config/nextflow.config
tags:
- adapterremoval
files:
- path: output/adapterremoval/test.discarded.gz
- path: output/adapterremoval/test.log
md5sum: 7f0b2328152226e46101a535cce718b3
- path: output/adapterremoval/test.merged.fastq.gz
md5sum: 07a8f725bfd3ecbeabdc41b32d898dee
md5sum: b8a451d3981b327f3fdb44f40ba2d6d1
- path: output/adapterremoval/test.pair1.truncated.gz
md5sum: 294a6277f0139bd597e57c6fa31f39c7
- path: output/adapterremoval/test.pair2.truncated.gz
md5sum: de7b38e2c881bced8671acb1ab452d78
- path: output/adapterremoval/test.singleton.truncated.gz
- path: output/adapterremoval/versions.yml
md5sum: fd428f92a8446e0b34c5ae1c447215b8