fix fasta_index_methylseq and fastq_align_dedup workflows #9496
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… and consistency - Updated variable names in fasta_index_methylseq to use 'channel' instead of 'Channel' for consistency. - Renamed UNTAR to UNTAR_BISMARK and UNTAR_BWAMETH for clarity in fasta_index_methylseq. - Enhanced comments and descriptions in meta.yml files for better understanding of input and output structures. - Adjusted test cases in fastq_align_dedup workflows to reflect changes in input structure from single-end to paired-end. - Updated version numbers in test snapshots to reflect recent changes.
sateeshperi
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eduard-watchmaker
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Dec 3, 2025
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All looks good to me, I will wait for the approval of the PR to implement fq2bam (gpu)
and thanks for the formatting and helping with consistency!
vagkaratzas
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Dec 8, 2025
* fix fasta_index_methylseq and fastq_align_dedup workflows for clarity and consistency - Updated variable names in fasta_index_methylseq to use 'channel' instead of 'Channel' for consistency. - Renamed UNTAR to UNTAR_BISMARK and UNTAR_BWAMETH for clarity in fasta_index_methylseq. - Enhanced comments and descriptions in meta.yml files for better understanding of input and output structures. - Adjusted test cases in fastq_align_dedup workflows to reflect changes in input structure from single-end to paired-end. - Updated version numbers in test snapshots to reflect recent changes. * fix: pre-commit lint fixes
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Closes #XXX