Closed nf-core-bot closed 5 months ago
OK I've started this now, things that I will need to re-add back in once I've done the template merge bit:
INPUT_CHECK
to new subworkflow, check that output channels (raw_short, raw_long etc.) are prepared correctly
--input
validation code// Ensure run IDs are unique within samples (also prevents duplicated sample names)
--assembly_input
validation codelib/
to the new subworkflow
WorkflowMag.nf
to validateInputPArametesmag.nf
get's appended to the end of the paramsSummaryLog()
nextflow_schema.json
update)[!IMPORTANT] Must document/announce no more direct input!
Test input files: template-merge-input-tests.zip
Test assembly input files:
template-merge-tests-assemblyinput.zip
--assembly_input
can only be used if --input
supplied--assembly_input
and --input
must match
validateInputParameters
how to deal with the odd hybrid
variable -> [FIXED] do the same as in current version (i.e., update the hybird
variable that is defined in the main script, from wtihin a map{}
) nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 41e8956
+| ✅ 212 tests passed |+
#| ❔ 2 tests were ignored |#
!| ❗ 5 tests had warnings |!
busco_failed_bins
to the email, users would discover this by looking at the results, and now we have checkM etc. which we dont' get the report it seems unnecessarily specific.It will reduce the load during future template merges
--input
must be suppilied if --assembly_input
supplied, as --input
is always requiredJust went through the code/ran some tests and this update looks great! Would probably be worth adding a test_assembly_input
profile, but that can probably be added when we implement nf-test
The failure on the test_binrefinement
test is apparently a gzipped FASTA file is getting through to cONCOCT cut-up-contigs and the python tool can't read GZIPPEd files
Fixed, finallY! :crossed_fingers: all good!
Version
2.13.1
of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the
nf-core-template-merge-2.13.1
branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.
For more information about this release of nf-core/tools, please see the
v2.13.1
release page.