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feat added stub to modules

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This commit is contained in:
Lucpen 2022-05-02 10:34:14 +02:00
parent 76ac37c529
commit 6b64f9cb6c
5 changed files with 61 additions and 0 deletions
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11
modules/gatk4/mergebamalignment/main.nf
View file

@ -43,4 +43,15 @@ process GATK4_MERGEBAMALIGNMENT {
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.bam
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}

14
modules/gatk4/mutect2/main.nf
View file

@ -57,4 +57,18 @@ process GATK4_MUTECT2 {
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.vcf.gz
touch ${prefix}.tbi
touch ${prefix}.stats
touch ${prefix}.f1r2.tar.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}

11
modules/gatk4/revertsam/main.nf
View file

@ -39,4 +39,15 @@ process GATK4_REVERTSAM {
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.reverted.bam
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}

13
modules/gatk4/samtofastq/main.nf
View file

@ -40,4 +40,17 @@ process GATK4_SAMTOFASTQ {
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.fastq.gz
touch ${prefix}_1.fastq.gz
touch ${prefix}_2.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}

12
modules/samtools/view/main.nf
View file

@ -41,4 +41,16 @@ process SAMTOOLS_VIEW {
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.bam
touch ${prefix}.cram
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}