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Merge pull request #104 from nf-core/motus-profile-update

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Update mOTUs profile module and mix log for multiqc
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James A. Fellows Yates 2022-07-14 16:03:01 +02:00 committed by GitHub
commit d7ca3df160
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5 changed files with 11 additions and 3 deletions
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1
conf/modules.config
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@ -391,6 +391,7 @@ process {
} }
withName: MOTUS_PROFILE { withName: MOTUS_PROFILE {
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/motus/${meta.db_name}" }, path: { "${params.outdir}/motus/${meta.db_name}" },
mode: params.publish_dir_mode mode: params.publish_dir_mode

2
modules.json
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@ -79,7 +79,7 @@
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
}, },
"motus/profile": { "motus/profile": {
"git_sha": "6b960f0e75bbb4d5bd301cd3875fa078d0eab4d1" "git_sha": "b6ed584443ad68ac41e6975994139454a4f23c18"
}, },
"multiqc": { "multiqc": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"

6
modules/nf-core/modules/motus/profile/main.nf generated
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@ -15,6 +15,7 @@ process MOTUS_PROFILE {
tuple val(meta), path("*.out"), emit: out tuple val(meta), path("*.out"), emit: out
tuple val(meta), path("*.bam"), optional: true, emit: bam tuple val(meta), path("*.bam"), optional: true, emit: bam
tuple val(meta), path("*.mgc"), optional: true, emit: mgc tuple val(meta), path("*.mgc"), optional: true, emit: mgc
tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:
@ -36,7 +37,8 @@ process MOTUS_PROFILE {
$refdb \\ $refdb \\
-t $task.cpus \\ -t $task.cpus \\
-n $prefix \\ -n $prefix \\
-o ${prefix}.out -o ${prefix}.out \\
2> ${prefix}.log
## mOTUs version number is not available from command line. ## mOTUs version number is not available from command line.
## mOTUs save the version number in index database folder. ## mOTUs save the version number in index database folder.
@ -48,7 +50,7 @@ process MOTUS_PROFILE {
fi fi
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
mOTUs: \$VERSION motus: \$VERSION
END_VERSIONS END_VERSIONS
""" """
} }

4
modules/nf-core/modules/motus/profile/meta.yml generated
View file

@ -56,6 +56,10 @@ output:
type: file type: file
description: Optional intermediate mgc read count table file saved with `-M`. description: Optional intermediate mgc read count table file saved with `-M`.
pattern: "*.{mgc}" pattern: "*.{mgc}"
- log:
type: file
description: Standard error logging file containing summary statistics
pattern: "*.log"
authors: authors:
- "@jianhong" - "@jianhong"

1
subworkflows/local/profiling.nf
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@ -227,6 +227,7 @@ workflow PROFILING {
MOTUS_PROFILE ( ch_input_for_motus.reads, ch_input_for_motus.db ) MOTUS_PROFILE ( ch_input_for_motus.reads, ch_input_for_motus.db )
ch_versions = ch_versions.mix( MOTUS_PROFILE.out.versions.first() ) ch_versions = ch_versions.mix( MOTUS_PROFILE.out.versions.first() )
ch_raw_profiles = ch_raw_profiles.mix( MOTUS_PROFILE.out.out ) ch_raw_profiles = ch_raw_profiles.mix( MOTUS_PROFILE.out.out )
ch_multiqc_files = ch_multiqc_files.mix( MOTUS_PROFILE.out.log.map{it[1]} )
} }