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chore: update adapterremoval

This commit is contained in:
Moritz E. Beber 2022-04-05 10:18:34 +02:00
parent fe628b3578
commit c54c32c494
3 changed files with 42 additions and 20 deletions

View file

@ -4,7 +4,7 @@
"repos": { "repos": {
"nf-core/modules": { "nf-core/modules": {
"adapterremoval": { "adapterremoval": {
"git_sha": "f0800157544a82ae222931764483331a81812012" "git_sha": "879d42c5e28661fe0a5e744c9e2c515868f9e08a"
}, },
"cat/fastq": { "cat/fastq": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"

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@ -12,14 +12,13 @@ process ADAPTERREMOVAL {
path(adapterlist) path(adapterlist)
output: output:
tuple val(meta), path("${prefix}.truncated.gz") , optional: true, emit: singles_truncated tuple val(meta), path("${prefix}.truncated.fastq.gz") , optional: true, emit: singles_truncated
tuple val(meta), path("${prefix}.discarded.gz") , optional: true, emit: discarded tuple val(meta), path("${prefix}.discarded.fastq.gz") , optional: true, emit: discarded
tuple val(meta), path("${prefix}.pair1.truncated.gz") , optional: true, emit: pair1_truncated tuple val(meta), path("${prefix}.pair{1,2}.truncated.fastq.gz") , optional: true, emit: paired_truncated
tuple val(meta), path("${prefix}.pair2.truncated.gz") , optional: true, emit: pair2_truncated tuple val(meta), path("${prefix}.collapsed.fastq.gz") , optional: true, emit: collapsed
tuple val(meta), path("${prefix}.collapsed.gz") , optional: true, emit: collapsed tuple val(meta), path("${prefix}.collapsed.truncated.fastq.gz") , optional: true, emit: collapsed_truncated
tuple val(meta), path("${prefix}.collapsed.truncated.gz") , optional: true, emit: collapsed_truncated tuple val(meta), path("${prefix}.paired.fastq.gz") , optional: true, emit: paired_interleaved
tuple val(meta), path("${prefix}.paired.gz") , optional: true, emit: paired_interleaved tuple val(meta), path('*.settings') , emit: settings
tuple val(meta), path('*.log') , emit: log
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:
@ -38,10 +37,19 @@ process ADAPTERREMOVAL {
$adapterlist \\ $adapterlist \\
--basename ${prefix} \\ --basename ${prefix} \\
--threads ${task.cpus} \\ --threads ${task.cpus} \\
--settings ${prefix}.log \\
--seed 42 \\ --seed 42 \\
--gzip --gzip
ensure_fastq() {
if [ -f "\${1}" ]; then
mv "\${1}" "\${1::-3}.fastq.gz"
fi
}
ensure_fastq '${prefix}.truncated.gz'
ensure_fastq '${prefix}.discarded.gz'
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g") adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
@ -56,10 +64,24 @@ process ADAPTERREMOVAL {
$adapterlist \\ $adapterlist \\
--basename ${prefix} \\ --basename ${prefix} \\
--threads $task.cpus \\ --threads $task.cpus \\
--settings ${prefix}.log \\
--seed 42 \\ --seed 42 \\
--gzip --gzip
ensure_fastq() {
if [ -f "\${1}" ]; then
mv "\${1}" "\${1::-3}.fastq.gz"
fi
}
ensure_fastq '${prefix}.truncated.gz'
ensure_fastq '${prefix}.discarded.gz'
ensure_fastq '${prefix}.pair1.truncated.gz'
ensure_fastq '${prefix}.pair2.truncated.gz'
ensure_fastq '${prefix}.collapsed.gz'
ensure_fastq '${prefix}.collapsed.truncated.gz'
ensure_fastq '${prefix}.paired.gz'
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g") adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")

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@ -43,43 +43,43 @@ output:
Adapter trimmed FastQ files of either single-end reads, or singleton 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 'orphaned' reads from merging of paired-end data (i.e., one of the pair
was lost due to filtering thresholds). was lost due to filtering thresholds).
pattern: "*.truncated.gz" pattern: "*.truncated.fastq.gz"
- discarded: - discarded:
type: file type: file
description: | description: |
Adapter trimmed FastQ files of reads that did not pass filtering Adapter trimmed FastQ files of reads that did not pass filtering
thresholds. thresholds.
pattern: "*.discarded.gz" pattern: "*.discarded.fastq.gz"
- pair1_truncated: - pair1_truncated:
type: file type: file
description: | description: |
Adapter trimmed R1 FastQ files of paired-end reads that did not merge 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 with their respective R2 pair due to long templates. The respective pair
is stored in 'pair2_truncated'. is stored in 'pair2_truncated'.
pattern: "*.pair1.truncated.gz" pattern: "*.pair1.truncated.fastq.gz"
- pair2_truncated: - pair2_truncated:
type: file type: file
description: | description: |
Adapter trimmed R2 FastQ files of paired-end reads that did not merge 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 with their respective R1 pair due to long templates. The respective pair
is stored in 'pair1_truncated'. is stored in 'pair1_truncated'.
pattern: "*.pair2.truncated.gz" pattern: "*.pair2.truncated.fastq.gz"
- collapsed: - collapsed:
type: file type: file
description: | description: |
Collapsed FastQ of paired-end reads that successfully merged with their Collapsed FastQ of paired-end reads that successfully merged with their
respective R1 pair but were not trimmed. respective R1 pair but were not trimmed.
pattern: "*.collapsed.gz" pattern: "*.collapsed.fastq.gz"
- collapsed_truncated: - collapsed_truncated:
type: file type: file
description: | description: |
Collapsed FastQ of paired-end reads that successfully merged with their Collapsed FastQ of paired-end reads that successfully merged with their
respective R1 pair and were trimmed of adapter due to sufficient overlap. respective R1 pair and were trimmed of adapter due to sufficient overlap.
pattern: "*.collapsed.truncated.gz" pattern: "*.collapsed.truncated.fastq.gz"
- log: - log:
type: file type: file
description: AdapterRemoval log file description: AdapterRemoval log file
pattern: "*.log" pattern: "*.settings"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions