Added hisat2 component #213
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@@ Coverage Diff @@
## master #213 +/- ##
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+ Coverage 41.95% 42.03% +0.07%
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Files 72 72
Lines 6461 6469 +8
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+ Hits 2711 2719 +8
Misses 3750 3750
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| """ | ||
| samtools view -Sb $sam > ${sample_id}.bam | ||
| samtools sort -T ${sample_id}.bam.tmp ${sample_id}.bam -o ${sample_id}.sorted.bam |
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You can improve I/O here by piping some of these commands: https://github.com/assemblerflow/flowcraft/blob/master/flowcraft/generator/templates/mapping_patlas.nf#L40 (example).
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Additionally, in your class you have defined the output as bam, not as bam, bai. This makes this component theoretically compatible with modules that receive bam files (retrieve_mapped, for example) but in fact they're not being compatible. Why don't you pass the .bai file as a side channel?
This change is