Swap ngscheckmate/ncm to nftest #5679
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| when { | ||
| process { | ||
| """ | ||
| input[0] = BCFTOOLS_MPILEUP1.out.vcf.combine(BCFTOOLS_MPILEUP2.out.vcf.map{it[1]}).map{meta, one, two -> [meta, [one, two]]}.map{meta, stuff -> [meta, stuff.flatten()]} |
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This is horrific and could do with cleaning up...
I have two outputs that are both:
[meta, vcf]
and I want to make
[new_meta, [vcf1, vcf2]]
* Swap ngscheckmate/ncm to nftest * Update main.nf.test
| setup { | ||
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| run("BEDTOOLS_MAKEWINDOWS") { | ||
| script "../../../bedtools/makewindows/main.nf" |
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That's a good point! Maybe this is something that can be handled by nf-core tools (@mirpedrol)
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Hmmm.
The alternative would be to add files to test_data instead, but there are quite a few modules that do this kind of setup block. This is essentially taking a bed file and splitting it into individual bases.
I guess BCFTOOLS_MPILEUP exists in sarek already, so you didn't have an issue with that part.
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BCFTOOLS_MPILEUP is installed in Sarek, so that didn't cause any issues. However, I guess the nf-test should be kind of self-contained, and not rely on what other modules might or might not be installed in the particular pipeline that is trying to use the module.
I also had to change all params.test_data... to params.modules_testdata_base_path... to get the test kind of work, that is, I managed to get 3 out of 4 "subtests" working:
Working on bringing NGSCheckMate modules to nf-test