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update genotyping libraries splitting for process names and saving
1 parent b7ac6ed commit 6eb67c4

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Lines changed: 23 additions & 20 deletions

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‎conf/modules.config‎

Lines changed: 23 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -515,6 +515,7 @@ process {
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]
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}
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518+
// TODO: add readgroup split for using unmerged libs for genotyping
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withName: 'BWA_SAMSE|BWA_SAMPE' {
519520
tag = { "${meta.id_index}|${meta.sample_id}_${meta.library_id}_L${meta.lane}" }
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ext.args = {
@@ -537,6 +538,7 @@ process {
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]
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}
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541+
// TODO: add readgroup split for using unmerged libs for genotyping
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withName: BWA_MEM {
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tag = { "${meta.reference}|${meta.sample_id}_${meta.library_id}_L${meta.lane}" }
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ext.args = {
@@ -552,6 +554,7 @@ process {
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]
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}
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557+
// TODO: add readgroup split for using unmerged libs for genotyping
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withName: BOWTIE2_ALIGN {
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tag = { "${meta.reference}|${meta.sample_id}_${meta.library_id}_L${meta.lane}" }
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ext.args = {
@@ -1260,7 +1263,6 @@ process {
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}
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withName: ".*MERGE_LIBRARIES_DAMAGE_MANIPULATION:SAMTOOLS_MERGE_LIBRARIES" {
1263-
// TODO: add parameter from run_trim_bam/run_pmd_filtering/run_mapdamage_rescaling --> replace genotpying source for final bams
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tag = { "${meta.reference}|${meta.sample_id}|${meta.damage_manipulation}" }
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ext.prefix = { "${meta.sample_id}_${meta.reference}_${meta.damage_manipulation}_unsorted" }
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publishDir = [
@@ -1639,22 +1641,22 @@ process {
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}
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withName: GATK_REALIGNERTARGETCREATOR {
1642-
tag = { "${meta.reference}|${meta.sample_id}" }
1644+
tag = { params.genotyping_use_unmerged_libraries ? "${meta.reference}|${meta.sample_id}|${meta.library_id}" : "${meta.reference}|${meta.sample_id}" }
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ext.args = [
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params.genotyping_gatk_ug_defaultbasequalities > 0 ? "--defaultBaseQualities ${params.genotyping_gatk_ug_defaultbasequalities}" : "", // Empty string since GATK complains if its default of -1 is provided.
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].join(' ').trim()
1646-
ext.prefix = { "${meta.sample_id}_${meta.reference}_realigntarget" }
1648+
ext.prefix = { params.genotyping_use_unmerged_libraries ? "${sample_id}_${meta.library_id}_${meta.reference}_realigntarget" : "${sample_id}_${meta.reference}_realigntarget" }
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publishDir = [
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enabled: false
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]
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}
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withName: GATK_INDELREALIGNER {
1653-
tag = { "${meta.reference}|${meta.sample_id}" }
1655+
tag = { params.genotyping_use_unmerged_libraries ? "${meta.reference}|${meta.sample_id}|${meta.library_id}" : "${meta.reference}|${meta.sample_id}" }
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ext.args = [
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params.genotyping_gatk_ug_defaultbasequalities > 0 ? "--defaultBaseQualities ${params.genotyping_gatk_ug_defaultbasequalities}" : "", // Empty string since GATK complains if its default of -1 is provided.
16561658
].join(' ').trim()
1657-
ext.prefix = { "${meta.sample_id}_${meta.reference}_realigned" }
1659+
ext.prefix = { params.genotyping_use_unmerged_libraries ? "${sample_id}_${meta.library_id}_${meta.reference}_realigned" : "${sample_id}_${meta.reference}_realigned" }
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publishDir = [
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[
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// data
@@ -1667,16 +1669,17 @@ process {
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}
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withName: GATK_UNIFIEDGENOTYPER {
1670-
tag = { "${meta.reference}|${meta.sample_id}" }
1672+
tag = { params.genotyping_use_unmerged_libraries ? "${meta.reference}|${meta.sample_id}|${meta.library_id}" : "${meta.reference}|${meta.sample_id}" }
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ext.args = {[
1672-
"--sample_ploidy ${meta2.ploidy}",
1674+
// ploidy set at 2 for non-specified ploidy in input fasta sheet for consistency with gatk default
1675+
meta2.ploidy ? "--sample_ploidy ${meta2.ploidy}" : "--sample_ploidy 2",
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"-stand_call_conf ${params.genotyping_gatk_call_conf}",
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"-dcov ${params.genotyping_gatk_ug_downsample}",
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"--output_mode ${params.genotyping_gatk_ug_out_mode}",
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"--genotype_likelihoods_model ${params.genotyping_gatk_ug_genotype_mode}",
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params.genotyping_gatk_ug_defaultbasequalities > 0 ? "--defaultBaseQualities ${params.genotyping_gatk_ug_defaultbasequalities}" : "", // Empty string since GATK complains if its default of -1 is provided.
16781681
].join(' ').trim() }
1679-
ext.prefix = { "${meta.sample_id}_${meta.reference}" }
1682+
ext.prefix = { params.genotyping_use_unmerged_libraries ? "${sample_id}_${meta.library_id}_${meta.reference}" : "${sample_id}_${meta.reference}" }
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publishDir = [
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[
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// data
@@ -1688,9 +1691,9 @@ process {
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}
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16901693
withName: BCFTOOLS_INDEX_UG {
1691-
tag = { "${meta.reference}|${meta.sample_id}" }
1694+
tag = { params.genotyping_use_unmerged_libraries ? "${meta.reference}|${meta.sample_id}|${meta.library_id}" : "${meta.reference}|${meta.sample_id}" }
16921695
ext.args = "--tbi" //tbi indices for consistency with GATK HC
1693-
ext.prefix = { "${meta.sample_id}_${meta.reference}" }
1696+
ext.prefix = { params.genotyping_use_unmerged_libraries ? "${sample_id}_${meta.library_id}_${meta.reference}" : "${sample_id}_${meta.reference}" }
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publishDir = [
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[
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// data
@@ -1702,15 +1705,15 @@ process {
17021705
}
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17041707
withName: GATK4_HAPLOTYPECALLER {
1705-
tag = { "${meta.reference}|${meta.sample_id}" }
1708+
tag = { params.genotyping_use_unmerged_libraries ? "${meta.reference}|${meta.sample_id}|${meta.library_id}" : "${meta.reference}|${meta.sample_id}" }
17061709
ext.args = {[
17071710
// Option names have changed from underscore_separated to hyphen-separated in GATK4
1708-
"--sample-ploidy ${meta2.ploidy}",
1711+
meta2.ploidy ? "--sample-ploidy ${meta2.ploidy}" : "--sample-ploidy 2",
17091712
"-stand-call-conf ${params.genotyping_gatk_call_conf}",
17101713
"--output-mode ${params.genotyping_gatk_hc_out_mode}",
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"--emit-ref-confidence ${params.genotyping_gatk_hc_emitrefconf}",
17121715
].join(' ').trim() }
1713-
ext.prefix = { "${meta.sample_id}_${meta.reference}" }
1716+
ext.prefix = { params.genotyping_use_unmerged_libraries ? "${sample_id}_${meta.library_id}_${meta.reference}" : "${sample_id}_${meta.reference}" }
17141717
publishDir = [
17151718
[
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// data
@@ -1722,13 +1725,13 @@ process {
17221725
}
17231726

17241727
withName: FREEBAYES {
1725-
tag = { "${meta.reference}|${meta.sample_id}" }
1728+
tag = { params.genotyping_use_unmerged_libraries ? "${meta.reference}|${meta.sample_id}|${meta.library_id}" : "${meta.reference}|${meta.sample_id}" }
17261729
ext.args = {[
1727-
"-p ${ref_meta.ploidy}",
1730+
ref_meta.ploidy ? "--ploidy ${ref_meta.ploidy}" : "--ploidy 2",
17281731
"-C ${params.genotyping_freebayes_min_alternate_count}",
17291732
params.genotyping_freebayes_skip_coverage != 0 ? "-g ${params.genotyping_freebayes_skip_coverage}" : "",
17301733
].join(' ').trim() }
1731-
ext.prefix = { "${meta.sample_id}_${meta.reference}" }
1734+
ext.prefix = { params.genotyping_use_unmerged_libraries ? "${sample_id}_${meta.library_id}_${meta.reference}" : "${sample_id}_${meta.reference}" }
17321735
publishDir = [
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[
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// data
@@ -1740,9 +1743,9 @@ process {
17401743
}
17411744

17421745
withName: BCFTOOLS_INDEX_FREEBAYES {
1743-
tag = { "${meta.reference}|${meta.sample_id}" }
1746+
tag = { params.genotyping_use_unmerged_libraries ? "${meta.reference}|${meta.sample_id}|${meta.library_id}" : "${meta.reference}|${meta.sample_id}" }
17441747
ext.args = "--tbi" //tbi indices for consistency with GATK HC
1745-
ext.prefix = { "${meta.sample_id}_${meta.reference}" }
1748+
ext.prefix = { params.genotyping_use_unmerged_libraries ? "${sample_id}_${meta.library_id}_${meta.reference}" : "${sample_id}_${meta.reference}" }
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publishDir = [
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[
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// data
@@ -1754,8 +1757,8 @@ process {
17541757
}
17551758

17561759
withName: BCFTOOLS_STATS_GENOTYPING {
1757-
tag = { "${meta.reference}|${meta.sample_id}" }
1758-
ext.prefix = { "${meta.sample_id}_${meta.reference}" }
1760+
tag = { params.genotyping_use_unmerged_libraries ? "${meta.reference}|${meta.sample_id}|${meta.library_id}" : "${meta.reference}|${meta.sample_id}" }
1761+
ext.prefix = { params.genotyping_use_unmerged_libraries ? "${sample_id}_${meta.library_id}_${meta.reference}" : "${sample_id}_${meta.reference}" }
17591762
publishDir = [
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[
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// stats

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