Nf test and fix dev #86
Conversation
ferenckata
left a comment
ferenckata
left a comment
There was a problem hiding this comment.
thanks for this! main point is that the samplesheet should be input for nf-core (infolder is also supported still, but there should be something called input), so those changes should be reverted back
check github actions, especially linting because those are easy to fix and would be nice to pass
| withName: INDEX_DEDUP { | ||
| publishDir = [ | ||
| path: { "${params.outdir}/samtools_index_dedup" }, | ||
| // path: { "${params.outdir}/samtools_index_dedup" }, |
There was a problem hiding this comment.
can you remove this line if we are not using it?
| withName: SAMTOOLS_DEDUP { | ||
| publishDir = [ | ||
| path: { "${params.outdir}/samtools_dedup" }, | ||
| // path: { "${params.outdir}/samtools_dedup" }, |
| genome_name: "sacCer3" | ||
| fasta: "testdata/sacCer3_genome/sacCer3.fa" | ||
| index: "testdata/sacCer3_genome/sacCer3_star_index/" | ||
| samplesheet: "/mnt/biggley/home/slava/projects/leancage_dev/pe_samplesheet.csv" |
There was a problem hiding this comment.
also samplesheet got renamed to input
| input: "docs/examples/samplesheet_sacer_pe.csv" | ||
| infolder: | ||
| sample_name_fields: | ||
| # mapping parameters |
There was a problem hiding this comment.
please add comment back, this is for the users as an example
| # CAGEr parameters | ||
| cager_sample_file: "docs/examples/sample_list.csv" # with sorted list of bigwigs, if mapping is run elsewhere | ||
| cager_sample_file: ../nepal_sample_list_test.csv |
| tssregion_up: -3000 | ||
| tssregion_down: 3000 | ||
| tsslogo_upstream: 35 | ||
| tsslogo_upstream: 20 |
| The parameters specific to mapping, can be left empty when running in `cageronly` mode: | ||
|
|
||
| - `input` specifies the input CSV samplesheet. This option is mutually exclusive with `infolder`. | ||
| - `samplesheet` specifies the input CSV samplesheet. This option is mutually exclusive with `infolder`. |
There was a problem hiding this comment.
it should be input, otherwise nfcore complains
| "description": "Genome annotation fiel in GTF format" | ||
| }, | ||
| "input": { | ||
| "samplesheet": { |
There was a problem hiding this comment.
check the github actions, it also shows the errors and warnings
| main: | ||
|
|
||
| if (params.input) { | ||
| if (params.samplesheet) { |
| bowtie2: true | ||
| # dedup | ||
| dedup: true | ||
| dist: 100 |
There was a problem hiding this comment.
i think this is not part of params, adjust schema and add with default parameters into the customcageq.nf file
Hi @ferenckata ,
I made sure that the full pipeline works with the default parameters and with some alternative parameters.
I'll address the issue of not providing a FASTA file in a couple weeks.
Could you please have a look and merge if it looks good to you?
Cheers,
Slava