ChIP-Seq Pipeline #22
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Add deeptools to the list of conda installs
#18) * chip-seq: Update "Aligner choice" with additional projects and details This splits projects into either "open source" or "description only". Under open source projects, this adds ENCODE's second version of their ChIP-seq pipeline (aptly named chip-seq-pipeline2), nf-core's ChIP-seq pipeline, and St. Jude's SEASEQ. Description only projects remain largely the same. Hard wraps in paragraphs were intentionally not included to be consistent with the rest of the document. * chip-seq: Update SEASEQ stable release version
Add read extension parameter to coverage generation
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@claymcleod - I can't assign you as a reviewer since you started this PR. |
a-frantz
reviewed
Sep 13, 2023
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| picard -Xmx${JAVA_HEAP_SIZE}g CleanSam \ | ||
| I=${BAM} \ # Input BAM. | ||
| O=${OUTPUT_FILENAME} # Output cleaned BAM |
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This should be Bash syntax, not WDL syntax
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| bamCoverage --bam ${MERGED_BAM} \ # Input BAM file | ||
| --outFileName ${PREFIX}.bw \ # Output bigwig filename | ||
| --outFileFormat bigwig \ # Set output format to bigwig | ||
| --numberOfProcessors "max" # Utilize all available processors |
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Bash syntax instead of WDL syntax
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Continuation of #16.
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