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Fix the coverage report, we were using the samtools flags for decont. instead of mapping #8

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merged 11 commits into from
Jun 3, 2024
Merged

Fix the coverage report, we were using the samtools flags for decont. instead of mapping #8

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a7ec1e7
Fix the coverage report, we were using the samtools flags for decont …
mberacochea May 30, 2024
6ed34e1
Use an alias for BWAMEM2_MEM_DECONT
mberacochea May 30, 2024
622773a
Forgot to used the renamed thingy
mberacochea May 30, 2024
d6119ea
Update samtools flag
mberacochea May 30, 2024
598d183
Update module diff
mberacochea May 30, 2024
3d294ef
Increate runtime limit to 8 hours for BWAMEM2_MEM_DECONT
mberacochea Jun 3, 2024
42d8a8a
Replaced reads_bwamem2_decontamination swf with the bwamem2decontnoba…
mberacochea Jun 3, 2024
04afe38
Adjust the modules.config
mberacochea Jun 3, 2024
bcfa37d
Adjust the memory reqs for the decontamination
mberacochea Jun 3, 2024
303026e
Fix config (meta2 replacement)
mberacochea Jun 3, 2024
5e9ba53
Change the decontaminated prefix
mberacochea Jun 3, 2024
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23 changes: 14 additions & 9 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -72,19 +72,24 @@ process {
]
}

withName: 'BWAMEM2_MEM' {
// This BWAMEM2_MEM belongs to the decontamination module
withName: 'BWAMEM2_MEM_DECONT' {
cpus = { check_max( 12 * task.attempt, 'cpus' ) }
memory = { check_max( 72.GB * task.attempt, 'memory' ) }
time = { check_max( 16.h * task.attempt, 'time' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
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ext.args = "-M"
ext.args2 = [
'-f',
'12',
'-F',
'256',
'-uS',
].join(' ').trim()
ext.args2 = "-f 12 -F 256 -uS"
}

// This BWAMEM2_MEM belongs to the coverage module
withName: 'BWAMEM2_MEM_COVERAGE' {
cpus = { check_max( 12 * task.attempt, 'cpus' ) }
memory = { check_max( 12.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }

ext.args = "-M"
ext.args2 = "-F 12 -F 256 -uS"
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}

withName: 'SAMTOOLS_BAM2FQ' {
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4 changes: 2 additions & 2 deletions subworkflows/ebi-metagenomics/reads_bwamem2_decontamination/main.nf
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
include { BWAMEM2_MEM } from '../../../modules/ebi-metagenomics/bwamem2/mem/main'
include { SAMTOOLS_BAM2FQ } from '../../../modules/ebi-metagenomics/samtools/bam2fq/main'
include { BWAMEM2_MEM as BWAMEM2_MEM_DECONT } from '../../../modules/ebi-metagenomics/bwamem2/mem/main'
include { SAMTOOLS_BAM2FQ } from '../../../modules/ebi-metagenomics/samtools/bam2fq/main'


workflow READS_BWAMEM2_DECONTAMINATION {
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12 changes: 6 additions & 6 deletions subworkflows/local/assembly_coverage.nf
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
include { BWAMEM2_INDEX } from '../../modules/nf-core/bwamem2/index/main'
include { BWAMEM2_MEM } from '../../modules/ebi-metagenomics/bwamem2/mem/main'
include { BWAMEM2_MEM as BWAMEM2_MEM_COVERAGE } from '../../modules/ebi-metagenomics/bwamem2/mem/main'
include { SAMTOOLS_IDXSTATS } from '../../modules/nf-core/samtools/idxstats/main'
include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../modules/nf-core/metabat2/jgisummarizebamcontigdepths/main'

Expand All @@ -19,21 +19,21 @@ workflow ASSEMBLY_COVERAGE {

ch_versions = ch_versions.mix(BWAMEM2_INDEX.out.versions)

BWAMEM2_MEM(
BWAMEM2_MEM_COVERAGE(
reads,
BWAMEM2_INDEX.out.index
)
ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions)

ch_versions = ch_versions.mix(BWAMEM2_MEM_COVERAGE.out.versions)

METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS(
BWAMEM2_MEM.out.bam
BWAMEM2_MEM_COVERAGE.out.bam
)

ch_versions = ch_versions.mix(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.versions)

SAMTOOLS_IDXSTATS(
BWAMEM2_MEM.out.bam
BWAMEM2_MEM_COVERAGE.out.bam
)

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ch_versions = ch_versions.mix(SAMTOOLS_IDXSTATS.out.versions)
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3 changes: 2 additions & 1 deletion workflows/miassembler.nf
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Expand Up @@ -120,7 +120,7 @@ workflow MIASSEMBLER {
- Paired-end reads are assembled with MetaSPAdes, unless specified otherwise
- An error is raised if the assembler and read layout are incompatible (shouldn't happen...)
*/
qc_reads_extended = READS_QC.out.qc_reads.map{ meta, reads ->
qc_reads_extended = READS_QC.out.qc_reads.map { meta, reads ->
if ( params.assembler == "megahit" || meta.single_end ) {
return [ meta + [assembler: "megahit", assembler_version: params.megahit_version], reads]
} else if ( ["metaspades", "spades"].contains(params.assembler) || !meta.single_end ) {
Expand All @@ -134,6 +134,7 @@ workflow MIASSEMBLER {
megahit: meta.assembler == "megahit"
xspades: ["metaspades", "spades"].contains(meta.assembler)
}.set { qc_reads }

ch_versions = ch_versions.mix(READS_QC.out.versions)

/******************/
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