Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

remove soft-linking of fasta instead stage in dir #7081

Merged
merged 4 commits into from
Nov 26, 2024
Merged

remove soft-linking of fasta instead stage in dir #7081

Show file tree
Hide file tree
Changes from 2 commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
608f44d
remove soft-linking of fasta instead stage in dir
sateeshperi Nov 25, 2024
c218126
Merge branch 'master' into fix/bismark-apps
sateeshperi Nov 25, 2024
6980020
add comments for fasta stageAs
sateeshperi Nov 26, 2024
22b12fa
Merge branch 'master' into fix/bismark-apps
sateeshperi Nov 26, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 4 additions & 6 deletions modules/nf-core/bismark/align/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ process BISMARK_ALIGN {

input:
tuple val(meta), path(reads)
tuple val(meta2), path(fasta)
tuple val(meta2), path(fasta, stageAs: 'tmp/*')
sateeshperi marked this conversation as resolved.
Show resolved Hide resolved
tuple val(meta3), path(index)

output:
Expand Down Expand Up @@ -56,13 +56,11 @@ process BISMARK_ALIGN {
}
}
"""
ln -sf \$(readlink $fasta) $index/$fasta

bismark \\
$fastq \\
--genome $index \\
${fastq} \\
--genome ${index} \\
--bam \\
$args
${args}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
12 changes: 4 additions & 8 deletions modules/nf-core/bismark/coverage2cytosine/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ process BISMARK_COVERAGE2CYTOSINE {

input:
tuple val(meta), path(coverage_file)
tuple val(meta2), path(fasta)
tuple val(meta2), path(fasta, stageAs: 'tmp/*')
sateeshperi marked this conversation as resolved.
Show resolved Hide resolved
tuple val(meta3), path(index)

output:
Expand All @@ -25,16 +25,12 @@ process BISMARK_COVERAGE2CYTOSINE {
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
if [ ! -f $index/$fasta ]; then
ln -s \$(readlink $fasta) $index/$fasta;
fi

coverage2cytosine \\
$coverage_file \\
--genome $index \\
${coverage_file} \\
--genome ${index} \\
--output ${prefix} \\
--gzip \\
$args
${args}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/bismark/deduplicate/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,9 +24,9 @@ process BISMARK_DEDUPLICATE {
def seqtype = meta.single_end ? '-s' : '-p'
"""
deduplicate_bismark \\
$args \\
$seqtype \\
--bam $bam
${args} \\
${seqtype} \\
--bam ${bam}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
4 changes: 1 addition & 3 deletions modules/nf-core/bismark/genomepreparation/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,11 +21,9 @@ process BISMARK_GENOMEPREPARATION {
def args = task.ext.args ?: ''
"""
bismark_genome_preparation \\
$args \\
${args} \\
BismarkIndex

rm $fasta

cat <<-END_VERSIONS > versions.yml
"${task.process}":
bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
Expand Down
12 changes: 7 additions & 5 deletions modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -102,7 +102,8 @@
"BS_GA.rev.2.bt2:md5,d36044c5dfe37af0411f60d446585bc6",
"genome_mfa.GA_conversion.fa:md5,e529375ec2039112161465b5169fcd59"
]
]
],
"genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6"
]
]
],
Expand Down Expand Up @@ -134,7 +135,8 @@
"BS_GA.rev.2.bt2:md5,d36044c5dfe37af0411f60d446585bc6",
"genome_mfa.GA_conversion.fa:md5,e529375ec2039112161465b5169fcd59"
]
]
],
"genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6"
]
]
],
Expand All @@ -144,9 +146,9 @@
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.1"
},
"timestamp": "2024-10-13T08:26:20.352083082"
"timestamp": "2024-11-25T15:32:55.125985002"
}
}
6 changes: 3 additions & 3 deletions modules/nf-core/bismark/methylationextractor/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -36,13 +36,13 @@ process BISMARK_METHYLATIONEXTRACTOR {
def seqtype = meta.single_end ? '-s' : '-p'
"""
bismark_methylation_extractor \\
$bam \\
${bam} \\
--bedGraph \\
--counts \\
--gzip \\
--report \\
$seqtype \\
$args
${seqtype} \\
${args}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/bismark/report/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ process BISMARK_REPORT {
script:
def args = task.ext.args ?: ''
"""
bismark2report $args
bismark2report ${args}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
Loading