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Fix BAM grouping failure due to lane field in metadata #70

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Fix BAM grouping failure due to lane field in metadata #70

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777eeae
Fixed trimmer in citation tool
RaqManzano Jan 13, 2026
8de4237
fix typo
RaqManzano Jan 15, 2026
e852619
Remove lane from meta
RaqManzano Feb 17, 2026
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4 changes: 2 additions & 2 deletions subworkflows/local/bam_align/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -144,7 +144,7 @@ workflow BAM_ALIGN {
}
// Manipulate meta map to remove old fields and add new ones
.map { meta, bam ->
[ meta - meta.subMap('id', 'read_group', 'data_type', 'num_lanes', 'read_group', 'size') + [ data_type: 'bam', id: meta.sample ], bam ]
[ meta - meta.subMap('id', 'read_group', 'data_type', 'num_lanes', 'read_group', 'size', 'lane') + [ data_type: 'bam', id: meta.sample ], bam ]
}
// Create groupKey from meta map
.map { meta, bam ->
Expand Down Expand Up @@ -176,7 +176,7 @@ workflow BAM_ALIGN {
}
// Manipulate meta map to remove old fields and add new ones
.map { meta, bam ->
[ meta - meta.subMap('id', 'read_group', 'data_type', 'num_lanes', 'read_group', 'size') + [ data_type: 'bam', id: meta.sample ], bam ]
[ meta - meta.subMap('id', 'read_group', 'data_type', 'num_lanes', 'read_group', 'size', 'lane') + [ data_type: 'bam', id: meta.sample ], bam ]
}
// Create groupKey from meta map
.map { meta, bam ->
Expand Down
4 changes: 2 additions & 2 deletions subworkflows/local/utils_nfcore_rnadnavar_pipeline/main.nf
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Expand Up @@ -207,7 +207,7 @@ def toolCitationText() {
// Build text sections for different pipeline components
def text_preprocessing = [
"Raw read quality control was performed with FastQC (Andrews 2010)",
params.trimmer == "fastp" ? "and preprocessing with fastp (Chen et al. 2018)." : "."
params.trim_fastq || params.split_fastq > 0 ? "and preprocessing with fastp (Chen et al. 2018)." : "."
].join(' ').trim()

def text_alignment = [
Expand Down Expand Up @@ -274,7 +274,7 @@ def toolBibliographyText() {
// Quality control and preprocessing
def qc_preprocessing_citations = [
"<li>Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/</li>",
params.trimmer == "fastp" ? "<li>Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep 1;34(17):i884-i890. <a href=\"https://doi.org/10.1093/bioinformatics/bty560\">10.1093/bioinformatics/bty560</a></li>" : ""
params.trim_fastq || params.split_fastq > 0 ? "<li>Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep 1;34(17):i884-i890. <a href=\"https://doi.org/10.1093/bioinformatics/bty560\">10.1093/bioinformatics/bty560</a></li>" : ""
].join(' ').trim()

// Alignment tools
Expand Down
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