The samplesheet and markersheet validation was previously written in python and run as a local module. Now the code has been ported to Groovy and moved into the PIPELINE_INITIALISATION workflow which aligns better with the nf-core style. Also the workflow parameter structure and channel content structures have been reworked to align better with the spirit of nf-core and generally tidied up.
PR checklist
[x] This comment contains a description of changes (with reason).
[x] Make sure your code lints (nf-core lint).
[x] Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
[x] Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
The samplesheet and markersheet validation was previously written in python and run as a local module. Now the code has been ported to Groovy and moved into the PIPELINE_INITIALISATION workflow which aligns better with the nf-core style. Also the workflow parameter structure and channel content structures have been reworked to align better with the spirit of nf-core and generally tidied up.
PR checklist
nf-core lint
).nf-test test main.nf.test -profile test,docker
).nextflow run . -profile debug,test,docker --outdir <OUTDIR>
).