Closed apeltzer closed 2 months ago
Just to note things down while they are fresh:
The CircularMapper step should actually be a subworkflow in the DSL2 version, as it encompasses multiple steps that have already existing modules (e.g. BWA Index, ALN, Samse/SAMPE, realignsamfile <-- module writing, samtools sort, samtools index)
Instead of the generator it should be:
CM_GENERATOR, BWA INDEX
Instead of having one step "mapper" it should be:
BWA_ALN, BWA_SAMSE/BWA_SAMPE, CM_REALIGNSAMFILE, SAMTOOLS_SORT, SAMTOOLS_INDEX
Done in https://github.com/nf-core/eager/blob/dev/subworkflows/local/circularmapper.nf
jfy133
commented
2 months ago
Just to note things down while they are fresh:
The CircularMapper step should actually be a subworkflow in the DSL2 version, as it encompasses multiple steps that have already existing modules (e.g. BWA Index, ALN, Samse/SAMPE, realignsamfile <-- module writing, samtools sort, samtools index)
Instead of the generator it should be:
CM_GENERATOR, BWA INDEX
Instead of having one step "mapper" it should be:
BWA_ALN, BWA_SAMSE/BWA_SAMPE, CM_REALIGNSAMFILE, SAMTOOLS_SORT, SAMTOOLS_INDEX