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Update bam2fastq10x to handle multiplexed samples #6702

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merged 5 commits into from
Oct 3, 2024
Merged

Update bam2fastq10x to handle multiplexed samples #6702

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1654c4d
update output dir for bamtofastq10x
Aug 15, 2024
7379f2a
update path for output fastq
Sep 13, 2024
38eebd0
update snapshot
Sep 27, 2024
2164bdd
update stub
Oct 2, 2024
5084659
update output definition in meta.yml
Oct 2, 2024
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9 changes: 5 additions & 4 deletions modules/nf-core/bamtofastq10x/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,8 @@ process BAMTOFASTQ10X {
tuple val(meta), path(bam)

output:
tuple val(meta), path("*.fastq.gz"), emit: fastq
path "versions.yml" , emit: versions
tuple val(meta), path("**/*.fastq.gz"), emit: fastq
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -24,7 +24,7 @@ process BAMTOFASTQ10X {
bamtofastq \\
$args \\
$bam \\
${prefix}.fastq.gz
$prefix

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand All @@ -35,7 +35,8 @@ process BAMTOFASTQ10X {
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.fastq.gz
mkdir -p ${prefix}/bamtofastq10x
touch ${prefix}/bamtofastq10x/bamtofastq.fastq.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
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4 changes: 2 additions & 2 deletions modules/nf-core/bamtofastq10x/meta.yml
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Expand Up @@ -37,10 +37,10 @@ output:
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1', single_end:false ]`
- "*.fastq.gz":
- "**/*.fastq.gz":
type: file
description: fastq compressed file
pattern: "*.fastq.gz"
pattern: "**/*.fastq.gz"
- versions:
- versions.yml:
type: file
Expand Down
22 changes: 9 additions & 13 deletions modules/nf-core/bamtofastq10x/tests/main.nf.test.snap
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Expand Up @@ -8,11 +8,9 @@
"id": "test"
},
[
[
"bamtofastq_S1_L000_I1_001.fastq.gz:md5,a33682ac881de7a7453d79721b7621a0",
"bamtofastq_S1_L000_R1_001.fastq.gz:md5,5ccebf77d8636d7a7cdfc59737aea79f",
"bamtofastq_S1_L000_R2_001.fastq.gz:md5,2ee7c90e4307deba74065cfd00a65002"
]
"bamtofastq_S1_L000_I1_001.fastq.gz:md5,a33682ac881de7a7453d79721b7621a0",
"bamtofastq_S1_L000_R1_001.fastq.gz:md5,5ccebf77d8636d7a7cdfc59737aea79f",
"bamtofastq_S1_L000_R2_001.fastq.gz:md5,2ee7c90e4307deba74065cfd00a65002"
]
]
],
Expand All @@ -25,11 +23,9 @@
"id": "test"
},
[
[
"bamtofastq_S1_L000_I1_001.fastq.gz:md5,a33682ac881de7a7453d79721b7621a0",
"bamtofastq_S1_L000_R1_001.fastq.gz:md5,5ccebf77d8636d7a7cdfc59737aea79f",
"bamtofastq_S1_L000_R2_001.fastq.gz:md5,2ee7c90e4307deba74065cfd00a65002"
]
"bamtofastq_S1_L000_I1_001.fastq.gz:md5,a33682ac881de7a7453d79721b7621a0",
"bamtofastq_S1_L000_R1_001.fastq.gz:md5,5ccebf77d8636d7a7cdfc59737aea79f",
"bamtofastq_S1_L000_R2_001.fastq.gz:md5,2ee7c90e4307deba74065cfd00a65002"
]
]
],
Expand All @@ -39,9 +35,9 @@
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.0"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-22T16:43:24.999397"
"timestamp": "2024-10-02T12:56:21.808042"
}
}
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