Best for publishDir to be explicitly on/off, and all modules (even when not publishing) need an ext.prefix, now that we don't have meta.id anymore.
Also ensure that all module configurations follow the code conventions (attribute order etc)
Results from quick check on 26/04/2024:
HOST_REMOVAL : has no ext.prefix
SAMTOOLS_INDEX_BAM_INPUT : has neither
SAMTOOLS_VIEW_GENOME: no ext.prefix
SAMTOOLS_INDEX_DAMAGE_RESCALED: no ext.prefix
SAMTOOLS_INDEX_DAMAGE_FILTERED: no ext.prefix
SAMTOOLS_INDEX_DAMAGE_TRIMMED: no ext.prefix
ANGSD_DOCOUNTS: wrong attribute order
MTNUCRATIO : no ext.prefix
QUALIMAP_BAMQC_WITHBED|QUALIMAP_BAMQC_NOBED: no ext.prefix
SAMTOOLS_DEPTH_SEXDETERRMINE: wrong attribute order
Best for publishDir to be explicitly on/off, and all modules (even when not publishing) need an ext.prefix, now that we don't have meta.id anymore. Also ensure that all module configurations follow the code conventions (attribute order etc)
Results from quick check on 26/04/2024:
HOST_REMOVAL: has no ext.prefixSAMTOOLS_INDEX_BAM_INPUT: has neitherSAMTOOLS_VIEW_GENOME: no ext.prefixSAMTOOLS_INDEX_DAMAGE_RESCALED: no ext.prefixSAMTOOLS_INDEX_DAMAGE_FILTERED: no ext.prefixSAMTOOLS_INDEX_DAMAGE_TRIMMED: no ext.prefixANGSD_DOCOUNTS: wrong attribute orderMTNUCRATIO: no ext.prefixQUALIMAP_BAMQC_WITHBED|QUALIMAP_BAMQC_NOBED: no ext.prefixSAMTOOLS_DEPTH_SEXDETERRMINE: wrong attribute order