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Tryin to fix bismark #6807

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Tryin to fix bismark #6807

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28 changes: 21 additions & 7 deletions modules/nf-core/bismark/genomepreparation/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ process BISMARK_GENOMEPREPARATION {
'biocontainers/bismark:0.24.2--hdfd78af_0' }"

input:
tuple val(meta), path(fasta)
tuple val(meta), path(fasta, name:"BismarkIndex/")

output:
tuple val(meta), path("BismarkIndex"), emit: index
Expand All @@ -20,14 +20,11 @@ process BISMARK_GENOMEPREPARATION {
script:
def args = task.ext.args ?: ''
"""
mkdir BismarkIndex
mv $fasta BismarkIndex/

bismark_genome_preparation \\
$args \\
BismarkIndex

rm BismarkIndex/$fasta
rm $fasta

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand All @@ -38,8 +35,25 @@ process BISMARK_GENOMEPREPARATION {
stub:
def args = task.ext.args ?: ''
"""
mkdir BismarkIndex
touch BismarkIndex/$fasta
rm $fasta

mkdir -p BismarkIndex/Bisulfite_Genome/CT_conversion
touch BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.1.bt2
touch BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.2.bt2
touch BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.3.bt2
touch BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.4.bt2
touch BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.rev.1.bt2
touch BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.rev.2.bt2
touch BismarkIndex/Bisulfite_Genome/CT_conversion/genome_mfa.CT_conversion.fa

mkdir -p BismarkIndex/Bisulfite_Genome/GA_conversion
touch BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.1.bt2
touch BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.2.bt2
touch BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.3.bt2
touch BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.4.bt2
touch BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.rev.1.bt2
touch BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.rev.2.bt2
touch BismarkIndex/Bisulfite_Genome/GA_conversion/genome_mfa.GA_conversion.fa

cat <<-END_VERSIONS > versions.yml
"${task.process}":
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44 changes: 41 additions & 3 deletions modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,26 @@
"id": "test"
},
[
"genome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
[
[
"BS_CT.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
"BS_CT.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
"BS_CT.3.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
"BS_CT.4.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
"BS_CT.rev.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
"BS_CT.rev.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
"genome_mfa.CT_conversion.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
],
[
"BS_GA.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
"BS_GA.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
"BS_GA.3.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
"BS_GA.4.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
"BS_GA.rev.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
"BS_GA.rev.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
"genome_mfa.GA_conversion.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
]
]
],
Expand All @@ -21,7 +40,26 @@
"id": "test"
},
[
"genome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
[
[
"BS_CT.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
"BS_CT.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
"BS_CT.3.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
"BS_CT.4.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
"BS_CT.rev.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
"BS_CT.rev.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
"genome_mfa.CT_conversion.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
],
[
"BS_GA.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
"BS_GA.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
"BS_GA.3.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
"BS_GA.4.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
"BS_GA.rev.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
"BS_GA.rev.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
"genome_mfa.GA_conversion.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
]
]
],
Expand All @@ -34,7 +72,7 @@
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-10-13T08:26:30.051110425"
"timestamp": "2024-10-18T15:50:44.009733"
},
"sarscov2 genome [fasta]": {
"content": [
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