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Merge remote-tracking branch 'origin/dev' into porechop-log

This commit is contained in:
James Fellows Yates 2022-07-29 09:51:34 +02:00
commit 873a13e028
7 changed files with 21 additions and 10 deletions

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@ -145,7 +145,7 @@ process {
publishDir = [
path: { "${params.outdir}/filtlong" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
pattern: '*.{fastq.gz,log}',
enabled: params.save_preprocessed_reads
]
}
@ -347,6 +347,7 @@ process {
}
withName: CENTRIFUGE_KREPORT {
errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'}
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
publishDir = [
@ -386,7 +387,7 @@ process {
publishDir = [
path: { "${params.outdir}/diamond/${meta.db_name}" },
mode: params.publish_dir_mode,
pattern: '*.{blast,xml,txt,daa,sam,tsv,paf}'
pattern: '*.{blast,xml,txt,daa,sam,tsv,paf,log}'
]
}

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@ -22,13 +22,13 @@
"git_sha": "d2726fcf75063960f06b36d2229a4c0966614108"
},
"centrifuge/kreport": {
"git_sha": "be4ae28c3c95b3c4047a7d9fb4cb0ed749631cea"
"git_sha": "734d0db6079a4aa43b6509b207e5d6feb35d4838"
},
"custom/dumpsoftwareversions": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"diamond/blastx": {
"git_sha": "bd3bfe0817246082525ab93707976676b1fe208b"
"git_sha": "3531824af826c16cd252bc5aa82ae169b244ebaa"
},
"fastp": {
"git_sha": "d0a1cbb703a130c19f6796c3fce24fbe7dfce789"

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@ -8,7 +8,7 @@ process CENTRIFUGE_KREPORT {
'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
input:
tuple val(meta), path(results)
tuple val(meta), path(report)
path db
output:
@ -23,7 +23,7 @@ process CENTRIFUGE_KREPORT {
def prefix = task.ext.prefix ?: "${meta.id}"
"""
db_name=`find -L ${db} -name "*.1.cf" -not -name "._*" | sed 's/.1.cf//'`
centrifuge-kreport -x \$db_name ${results} > ${prefix}.txt
centrifuge-kreport -x \$db_name ${report} > ${prefix}.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":

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@ -15,9 +15,9 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- results:
- report:
type: file
description: File containing the centrifuge classification results
description: File containing the centrifuge classification report
pattern: "*.{txt}"
output:

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@ -21,6 +21,7 @@ process DIAMOND_BLASTX {
tuple val(meta), path('*.sam') , optional: true, emit: sam
tuple val(meta), path('*.tsv') , optional: true, emit: tsv
tuple val(meta), path('*.paf') , optional: true, emit: paf
tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions
when:
@ -54,7 +55,10 @@ process DIAMOND_BLASTX {
--query $fasta \\
--outfmt ${outfmt} ${columns} \\
$args \\
--out ${prefix}.${out_ext}
--out ${prefix}.${out_ext} \\
--log
mv diamond.log ${prefix}.log
cat <<-END_VERSIONS > versions.yml
"${task.process}":

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@ -70,7 +70,12 @@ output:
type: file
description: File containing software versions
pattern: "versions.yml"
- log:
type: file
description: Log file containing stdout information
pattern: "*.{log}"
authors:
- "@spficklin"
- "@jfy133"
- "@mjamy"

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@ -148,7 +148,7 @@ workflow PROFILING {
}
CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_reads, params.centrifuge_save_reads, params.centrifuge_save_reads )
CENTRIFUGE_KREPORT (CENTRIFUGE_CENTRIFUGE.out.results, ch_input_for_centrifuge.db)
CENTRIFUGE_KREPORT (CENTRIFUGE_CENTRIFUGE.out.report, ch_input_for_centrifuge.db)
ch_versions = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
ch_raw_classifications = ch_raw_classifications.mix( CENTRIFUGE_CENTRIFUGE.out.results )
ch_raw_profiles = ch_raw_profiles.mix( CENTRIFUGE_KREPORT.out.kreport )
@ -208,6 +208,7 @@ workflow PROFILING {
DIAMOND_BLASTX ( ch_input_for_diamond.reads, ch_input_for_diamond.db, ch_diamond_reads_format , [] )
ch_versions = ch_versions.mix( DIAMOND_BLASTX.out.versions.first() )
ch_raw_profiles = ch_raw_profiles.mix( DIAMOND_BLASTX.out.tsv )
ch_multiqc_files = ch_multiqc_files.mix( DIAMOND_BLASTX.out.log )
}