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feat: remove hacky INDEX #1222

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feat: remove hacky INDEX #1222

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f524d06
feat: remove hacky INDEX
maxulysse Jan 20, 2022
6316357
feat: even better
maxulysse Jan 20, 2022
edbb6ce
Merge branch 'master' into master_better_index
maxulysse Jan 20, 2022
8008433
Merge branch 'master' into master_better_index
maxulysse Jan 21, 2022
cd761be
Merge branch 'master' into master_better_index
maxulysse Feb 4, 2022
248936a
Merge branch 'master' into master_better_index
maxulysse Mar 28, 2022
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2 changes: 1 addition & 1 deletion modules/bwa/index/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ process BWA_INDEX {
path fasta

output:
path "bwa" , emit: index
path "bwa/*" , emit: index
path "versions.yml", emit: versions

script:
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4 changes: 1 addition & 3 deletions modules/bwa/mem/main.nf
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Expand Up @@ -23,13 +23,11 @@ process BWA_MEM {
def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
def samtools_command = sort_bam ? 'sort' : 'view'
"""
INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`

bwa mem \\
$args \\
$read_group \\
-t $task.cpus \\
\$INDEX \\
${index[0].baseName} \\
$reads \\
| samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam -

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7 changes: 4 additions & 3 deletions modules/bwamem2/index/main.nf
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Expand Up @@ -11,8 +11,8 @@ process BWAMEM2_INDEX {
path fasta

output:
path "bwamem2" , emit: index
path "versions.yml" , emit: versions
path "bwamem2/*" , emit: index
path "versions.yml", emit: versions

script:
def args = task.ext.args ?: ''
Expand All @@ -21,7 +21,8 @@ process BWAMEM2_INDEX {
bwa-mem2 \\
index \\
$args \\
$fasta -p bwamem2/${fasta}
-p bwamem2/${fasta} \\
$fasta

cat <<-END_VERSIONS > versions.yml
"${task.process}":
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4 changes: 1 addition & 3 deletions modules/bwamem2/mem/main.nf
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Expand Up @@ -23,14 +23,12 @@ process BWAMEM2_MEM {
def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
def samtools_command = sort_bam ? 'sort' : 'view'
"""
INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`

bwa-mem2 \\
mem \\
$args \\
$read_group \\
-t $task.cpus \\
\$INDEX \\
${index[0].baseName} \\
$reads \\
| samtools $samtools_command $args2 -@ $task.cpus -o ${prefix}.bam -

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