Bam support#129
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apeltzer merged 9 commits intonf-core:devfrom Jan 25, 2019
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| if( params.singleEnd || params.pairedEnd || params.bam){ | ||
| } else { | ||
| exit 1, "Please specify either --singleEnd or --pairedEnd to execute the pipeline!" | ||
| exit 1, "Please specify either --singleEnd, --pairedEnd to execute the pipeline on FastQ files and --bam for previously mapped BAM files!" |
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previously processed (not necessarily mapped in some cases...)
jfy133
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Looks provisionally good to me, small suggestion to tweak bam input help/error message
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This adds support for BAM input in general, please test this :-)
#41
Future TSV/CSV input will be a bit different in handling, also I might need to polish the codebase soon a bit, not too happy how I had to do this:
PR checklist
nextflow run . -profile test,docker).nf-core lint .).docsis updatedCHANGELOG.mdis updated