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Update mergebam syntax and sample specific unmapped channel (#1238)

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* initial commit to setup branch

* workflow finished

* Update nextflow.config

* tumour to tumor, getpileup passed as nomral and tumor

* paired_somatic renamed to tumor_normal_somatic

* Apply suggestions from code review

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* updated index names in meta.yml

* changed index file names in main script and test

* Apply suggestions from code review

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* Apply suggestions from code review

* fixed bug from changes

* Apply suggestions from code review

* modified yml to allow new subworkflow testing

* Update test.yml

* Update test.yml

* updated to follow the new mergebam syntax, also made unaligned input sample specific

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
This commit is contained in:
GCJMackenzie 2022-01-27 15:30:27 +00:00 committed by GitHub
parent d70526c806
commit 08db860938
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2 changed files with 8 additions and 9 deletions
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11
modules/gatk4/mergebamalignment/main.nf
View file

@ -8,8 +8,7 @@ process GATK4_MERGEBAMALIGNMENT {
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(aligned)
path unmapped
tuple val(meta), path(aligned), path(unmapped)
path fasta
path dict
@ -28,10 +27,10 @@ process GATK4_MERGEBAMALIGNMENT {
}
"""
gatk --java-options "-Xmx${avail_mem}g" MergeBamAlignment \\
ALIGNED=$aligned \\
UNMAPPED=$unmapped \\
R=$fasta \\
O=${prefix}.bam \\
-ALIGNED $aligned \\
-UNMAPPED $unmapped \\
-R $fasta \\
-O ${prefix}.bam \\
$args
cat <<-END_VERSIONS > versions.yml

6
tests/modules/gatk4/mergebamalignment/main.nf
View file

@ -6,11 +6,11 @@ include { GATK4_MERGEBAMALIGNMENT } from '../../../../modules/gatk4/mergebamalig
workflow test_gatk4_mergebamalignment {
input = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
]
unmapped = file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
GATK4_MERGEBAMALIGNMENT ( input, unmapped, fasta, dict )
GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
}