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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,145 +1,184 @@ | ||
| # TODO What do we do with these? | ||
| # I think we can require Docker,modules,Shard 1..Singularity,subworkflows,3 and skip the condas now | ||
| # - path: modules/nf-core/nf-test | ||
| # - profile: conda | ||
| # path: modules/nf-core/angsd/gl | ||
| # - profile: conda | ||
| # path: modules/nf-core/annotsv/installannotations | ||
| # - profile: conda | ||
| # path: modules/nf-core/happy/sompy | ||
| # - profile: conda | ||
| # path: modules/nf-core/backsub | ||
| # - profile: conda | ||
| # path: modules/nf-core/bakta/bakta | ||
| # - profile: conda | ||
| # path: modules/nf-core/bakta/baktadbdownload | ||
| # - profile: conda | ||
| # path: modules/nf-core/bases2fastq | ||
| # - profile: conda | ||
| # path: modules/nf-core/bcl2fastq | ||
| # - profile: conda | ||
| # path: modules/nf-core/bclconvert | ||
| # - profile: conda | ||
| # path: modules/nf-core/celesta | ||
| # - profile: conda | ||
| # path: modules/nf-core/cellpose | ||
| # - profile: conda | ||
| # path: modules/nf-core/cellranger/count | ||
| # - profile: conda | ||
| # path: modules/nf-core/cellranger/mkfastq | ||
| # - profile: conda | ||
| # path: modules/nf-core/cellranger/mkgtf | ||
| # - profile: conda | ||
| # path: modules/nf-core/cellranger/mkref | ||
| # - profile: conda | ||
| # path: modules/nf-core/cellranger/mkvdjref | ||
| # - profile: conda | ||
| # path: modules/nf-core/cellranger/multi | ||
| # - profile: conda | ||
| # path: modules/nf-core/cellranger/vdj | ||
| # - profile: conda | ||
| # path: modules/nf-core/checkqc | ||
| # - profile: conda | ||
| # path: modules/nf-core/custom/dumpsoftwareversions | ||
| # - profile: conda | ||
| # path: modules/nf-core/deepcell/mesmer | ||
| # - profile: conda | ||
| # path: modules/nf-core/deepvariant | ||
| - profile: conda | ||
| path: modules/nf-core/deepvariant/callvariants | ||
| - profile: conda | ||
| path: modules/nf-core/deepvariant/makeexamples | ||
| - profile: conda | ||
| path: modules/nf-core/deepvariant/postprocessvariants | ||
| - profile: conda | ||
| path: modules/nf-core/deepvariant/rundeepvariant | ||
| # - profile: conda | ||
| # path: modules/nf-core/ensemblvep/vep | ||
| # - profile: conda | ||
| # path: modules/nf-core/fastk/fastk | ||
| # - profile: conda | ||
| # path: modules/nf-core/fastk/histex | ||
| # - profile: conda | ||
| # path: modules/nf-core/fastk/merge | ||
| # - profile: conda | ||
| # path: modules/nf-core/fcs/fcsadaptor | ||
| # - profile: conda | ||
| # path: modules/nf-core/fcs/fcsgx | ||
| # - profile: conda | ||
| # path: modules/nf-core/ganon/buildcustom | ||
| # - profile: conda | ||
| # path: modules/nf-core/ganon/classify | ||
| # - profile: conda | ||
| # path: modules/nf-core/ganon/report | ||
| # - profile: conda | ||
| # path: modules/nf-core/ganon/table | ||
| # - profile: conda | ||
| # path: modules/nf-core/gatk4/cnnscorevariants | ||
| # - profile: conda | ||
| # path: modules/nf-core/gatk4/determinegermlinecontigploidy | ||
| # - profile: conda | ||
| # path: modules/nf-core/genescopefk | ||
| # - profile: conda | ||
| # path: modules/nf-core/ilastik/multicut | ||
| # - profile: conda | ||
| # path: modules/nf-core/ilastik/pixelclassification | ||
| # - profile: conda | ||
| # path: modules/nf-core/imputeme/vcftoprs | ||
| # - profile: conda | ||
| # path: modules/nf-core/mcquant | ||
| # - profile: conda | ||
| # path: modules/nf-core/merquryfk/katcomp | ||
| # - profile: conda | ||
| # path: modules/nf-core/merquryfk/katgc | ||
| # - profile: conda | ||
| # path: modules/nf-core/merquryfk/merquryfk | ||
| # - profile: conda | ||
| # path: modules/nf-core/merquryfk/ploidyplot | ||
| # - profile: conda | ||
| # path: modules/nf-core/molkartgarage/clahe | ||
| # - profile: conda | ||
| # path: modules/nf-core/quartonotebook | ||
| # - profile: conda | ||
| # path: modules/nf-core/scimap/spatiallda | ||
| # - profile: conda | ||
| # path: modules/nf-core/sentieon/bwaindex | ||
| # - profile: conda | ||
| # path: modules/nf-core/sentieon/bwamem | ||
| - profile: conda | ||
| path: modules/nf-core/sentieon/datametrics | ||
| # - profile: conda | ||
| # path: modules/nf-core/sentieon/dedup | ||
| # - profile: conda | ||
| # path: modules/nf-core/sentieon/qualcal | ||
| # - profile: conda | ||
| # path: modules/nf-core/spaceranger/mkgtf | ||
| # - profile: conda | ||
| # path: modules/nf-core/spaceranger/mkref | ||
| # - profile: conda | ||
| # path: modules/nf-core/spaceranger/count | ||
| # - profile: conda | ||
| # path: modules/nf-core/spotiflow | ||
| # - profile: conda | ||
| # path: modules/nf-core/svanalyzer/svbenchmark | ||
| # - profile: conda | ||
| # path: modules/nf-core/universc | ||
| # - profile: singularity | ||
| # path: modules/nf-core/universc | ||
| # - profile: conda | ||
| # path: modules/nf-core/vt/decompose | ||
| # - profile: singularity | ||
| # path: modules/nf-core/bases2fastq | ||
| # - profile: conda | ||
| # path: modules/nf-core/wittyer | ||
| # - profile: conda | ||
| # path: modules/nf-core/islandpath | ||
| # - profile: conda | ||
| # path: subworkflows/nf-core/vcf_annotate_ensemblvep | ||
| # - profile: conda | ||
| # path: subworkflows/nf-core/bcl_demultiplex | ||
| - profile: conda | ||
| path: subworkflows/nf-core/deepvariant | ||
| # - profile: conda | ||
| # path: subworkflows/nf-core/fastq_align_bamcmp_bwa | ||
| # - profile: conda | ||
| # path: subworkflows/nf-core/fastq_align_bwa | ||
| exclude: | ||
| - path: modules/nf-core/nf-test | ||
| - profile: conda | ||
| path: modules/nf-core/angsd/gl | ||
| - profile: conda | ||
| path: modules/nf-core/annotsv/installannotations | ||
| - profile: conda | ||
| path: modules/nf-core/happy/sompy | ||
| - profile: conda | ||
| path: modules/nf-core/backsub | ||
| - profile: conda | ||
| path: modules/nf-core/bakta/bakta | ||
| - profile: conda | ||
| path: modules/nf-core/bakta/baktadbdownload | ||
| - profile: conda | ||
| path: modules/nf-core/bases2fastq | ||
| - profile: conda | ||
| path: modules/nf-core/bcl2fastq | ||
| - profile: conda | ||
| path: modules/nf-core/bclconvert | ||
| - profile: conda | ||
| path: modules/nf-core/celesta | ||
| - profile: conda | ||
| path: modules/nf-core/cellpose | ||
| - profile: conda | ||
| path: modules/nf-core/cellranger/count | ||
| - profile: conda | ||
| path: modules/nf-core/cellranger/mkfastq | ||
| - profile: conda | ||
| path: modules/nf-core/cellranger/mkgtf | ||
| - profile: conda | ||
| path: modules/nf-core/cellranger/mkref | ||
| - profile: conda | ||
| path: modules/nf-core/cellranger/mkvdjref | ||
| - profile: conda | ||
| path: modules/nf-core/cellranger/multi | ||
| - profile: conda | ||
| path: modules/nf-core/cellranger/vdj | ||
| - profile: conda | ||
| path: modules/nf-core/checkqc | ||
| - profile: conda | ||
| path: modules/nf-core/custom/dumpsoftwareversions | ||
| - profile: conda | ||
| path: modules/nf-core/deepcell/mesmer | ||
| - profile: conda | ||
| path: modules/nf-core/deepsomatic | ||
| - profile: singularity | ||
| path: modules/nf-core/deepsomatic | ||
| - profile: conda | ||
| path: modules/nf-core/deepvariant | ||
| - profile: conda | ||
| path: modules/nf-core/deepvariant/callvariants | ||
| - profile: conda | ||
| path: modules/nf-core/deepvariant/makeexamples | ||
| - profile: conda | ||
| path: modules/nf-core/deepvariant/postprocessvariants | ||
| - profile: conda | ||
| path: modules/nf-core/deepvariant/rundeepvariant | ||
| - profile: conda | ||
| path: modules/nf-core/deepvariant/vcfstatsreport | ||
| - profile: conda | ||
| path: modules/nf-core/doubletdetection | ||
| - profile: conda | ||
| path: modules/nf-core/ensemblvep/vep | ||
| - profile: conda | ||
| path: modules/nf-core/fastk/fastk | ||
| - profile: conda | ||
| path: modules/nf-core/cellrangerarc/mkgtf | ||
| - profile: conda | ||
| path: modules/nf-core/fastk/histex | ||
| - profile: conda | ||
| path: modules/nf-core/fastk/merge | ||
| - profile: conda | ||
| path: modules/nf-core/fcs/fcsadaptor | ||
| - profile: conda | ||
| path: modules/nf-core/fcs/fcsgx | ||
| - profile: conda | ||
| path: modules/nf-core/ganon/buildcustom | ||
| - profile: conda | ||
| path: modules/nf-core/ganon/classify | ||
| - profile: conda | ||
| path: modules/nf-core/ganon/report | ||
| - profile: conda | ||
| path: modules/nf-core/ganon/table | ||
| - profile: conda | ||
| path: modules/nf-core/gatk4/cnnscorevariants | ||
| - profile: conda | ||
| path: modules/nf-core/gatk4/determinegermlinecontigploidy | ||
| - profile: conda | ||
| path: modules/nf-core/genescopefk | ||
| - profile: conda | ||
| path: modules/nf-core/ilastik/multicut | ||
| - profile: conda | ||
| path: modules/nf-core/ilastik/pixelclassification | ||
| - profile: conda | ||
| path: modules/nf-core/imputeme/vcftoprs | ||
| - profile: conda | ||
| path: modules/nf-core/mcstaging/imc2mc | ||
| - profile: conda | ||
| path: modules/nf-core/mcquant | ||
| - profile: conda | ||
| path: modules/nf-core/mcstaging/phenoimager2mc | ||
| - profile: conda | ||
| path: modules/nf-core/merquryfk/katcomp | ||
| - profile: conda | ||
| path: modules/nf-core/merquryfk/katgc | ||
| - profile: conda | ||
| path: modules/nf-core/merquryfk/merquryfk | ||
| - profile: conda | ||
| path: modules/nf-core/merquryfk/ploidyplot | ||
| - profile: conda | ||
| path: modules/nf-core/molkartgarage/clahe | ||
| - profile: conda | ||
| path: modules/nf-core/quartonotebook | ||
| - profile: conda | ||
| path: modules/nf-core/scimap/spatiallda | ||
| - profile: conda | ||
| path: modules/nf-core/sentieon/bwaindex | ||
| - profile: conda | ||
| path: modules/nf-core/sentieon/bwamem | ||
| - profile: conda | ||
| path: modules/nf-core/sentieon/datametrics | ||
| - profile: conda | ||
| path: modules/nf-core/sentieon/dedup | ||
| - profile: conda | ||
| path: modules/nf-core/sentieon/qualcal | ||
| - profile: conda | ||
| path: modules/nf-core/spaceranger/mkgtf | ||
| - profile: conda | ||
| path: modules/nf-core/spaceranger/mkref | ||
| - profile: conda | ||
| path: modules/nf-core/spaceranger/count | ||
| - profile: conda | ||
| path: modules/nf-core/spotiflow | ||
| - profile: conda | ||
| path: modules/nf-core/svanalyzer/svbenchmark | ||
| - profile: conda | ||
| path: modules/nf-core/universc | ||
| - profile: singularity | ||
| path: modules/nf-core/universc | ||
| - profile: conda | ||
| path: modules/nf-core/vt/decompose | ||
| - profile: singularity | ||
| path: modules/nf-core/bases2fastq | ||
| - profile: conda | ||
| path: modules/nf-core/wittyer | ||
| - profile: conda | ||
| path: modules/nf-core/islandpath | ||
| - profile: conda | ||
| path: modules/nf-core/scimap/mcmicro | ||
| - profile: conda | ||
| path: modules/nf-core/parabricks/fq2bammeth | ||
| - profile: docker_self_hosted | ||
| path: modules/nf-core/parabricks/fq2bammeth | ||
| - profile: singularity | ||
| path: modules/nf-core/parabricks/fq2bammeth | ||
| - profile: conda | ||
| path: modules/nf-core/parabricks/fq2bam | ||
| - profile: docker_self_hosted | ||
| path: modules/nf-core/parabricks/fq2bam | ||
| - profile: singularity | ||
| path: modules/nf-core/parabricks/fq2bam | ||
| - profile: conda | ||
| path: subworkflows/nf-core/vcf_annotate_ensemblvep | ||
| - profile: conda | ||
| path: subworkflows/nf-core/bcl_demultiplex | ||
| - profile: conda | ||
| path: subworkflows/nf-core/deepvariant | ||
| - profile: conda | ||
| path: subworkflows/nf-core/fastq_align_bamcmp_bwa | ||
| - profile: conda | ||
| path: subworkflows/nf-core/fastq_align_bwa | ||
| - profile: conda | ||
| path: subworkflows/nf-core/fasta_newick_epang_gappa | ||
| - profile: conda | ||
| path: modules/nf-core/xeniumranger/relabel | ||
| - profile: conda | ||
| path: modules/nf-core/xeniumranger/rename | ||
| - profile: conda | ||
| path: modules/nf-core/xeniumranger/resegment | ||
| - profile: conda | ||
| path: modules/nf-core/xeniumranger/import-segmentation |
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