Chipseq updates #111
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Chipseq updates #111
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a-frantz
requested changes
Sep 25, 2023
|
@adthrasher can you split the |
Moved to #119 |
adthrasher
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Nov 7, 2023
a-frantz
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Nov 22, 2023
* main: feat: Style updates (#122) fix: calc_gene_length algorithm. And better docs for gene length and TPM (#120) Iterative samtools merge (#118) chore: move from pr #111 (#119) feat: experimental dnaseq-standard WF (#116) docs: new stuff for style-guide, best-practices, and template (#117) docs: More docs (#114) fix(qc): finish deleting gc_bias_metrics feat(qc): drop requirement of reference_fasta feat: put strandedness value into HTSeq file name (#90) chore: bump all kraken images to latest (#113)
adthrasher
commented
Sep 26, 2024
| max_retries=max_retries | ||
| } | ||
| String rg_id_field = sub(sub(pair.right, ".*ID:", "ID:"), "\t.*", "") | ||
| String rg_id_field = sub(sub(tuple.right, ".*ID:", "ID:"), "\t.*", "") | ||
| String rg_id = sub(rg_id_field, "ID:", "") | ||
| call samtools.addreplacerg as single_end { input: |
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Rename single_end to something else
a-frantz
reviewed
Feb 7, 2025
Comment on lines
+151
to
+156
| "MISSING_PLATFORM_VALUE", | ||
| "INVALID_PLATFORM_VALUE", | ||
| "INVALID_MAPPING_QUALITY", | ||
| "MATES_ARE_SAME_END", | ||
| "MISMATCH_FLAG_MATE_NEG_STRAND", | ||
| "MISMATCH_MATE_ALIGNMENT_START" |
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The first two seem "ok" to ignore. Less comfortable ignoring the last four. Are all these still being produced by seaseq?
| max_retries=max_retries | ||
| } | ||
| String rg_id_field = sub(sub(pair.right, ".*ID:", "ID:"), "\t.*", "") | ||
| String rg_id_field = sub(sub(tuple.right, ".*ID:", "ID:"), "\t.*", "") | ||
| String rg_id = sub(rg_id_field, "ID:", "") | ||
| call samtools.addreplacerg as single_end { input: |
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Updates to reflect changes to SEAseq and add support for SEAseq's paired-end mode.