Remove merging of individuals for now and add it to road map

nf-core · Apr 23, 2024 · 9d21a5d · 9d21a5d
1 parent 870c63e
commit 9d21a5d
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diff --git a/docs/development.md b/docs/development.md
@@ -17,6 +17,7 @@
 - [] Check if panel is necessary depending on the tool selected
 - [x] Set modules configuration as full path workflow:subworkflow:module
 - [] Where should the map file go (separate csv or in panel csv)
+- [] Add support for imputation by individuals or by groups of individuals
 
 ## Run tests
 
@@ -25,6 +26,7 @@ nextflow run main.nf -profile singularity,test --outdir results -resume
 nextflow run main.nf -profile singularity,test_sim --outdir results -resume
 nextflow run main.nf -profile singularity,test_validate --outdir results -resume
 nextflow run main.nf -profile singularity,test_all --outdir results -resume
+nextflow run main.nf -profile singularity,test_quilt --outdir results -resume
 ```
 
 ## Problematic

diff --git a/workflows/phaseimpute/main.nf b/workflows/phaseimpute/main.nf
@@ -177,13 +177,8 @@ workflow PHASEIMPUTE {
                     // Create chunks from reference VCF
                     MAKE_CHUNKS(ch_panel, ch_fasta)
 
-                    // Create input QUILT
-                    ch_input_quilt = ch_input_impute
-                                .map { meta, bam, bai -> [["id": "all_samples"] + meta.subMap("chr", "region"), bam, bai] }
-                                .groupTuple ()
-
                     // Impute BAMs with QUILT
-                    IMPUTE_QUILT(MAKE_CHUNKS.out.ch_hap_legend, ch_input_quilt, MAKE_CHUNKS.out.ch_chunks)
+                    IMPUTE_QUILT(MAKE_CHUNKS.out.ch_hap_legend, ch_input_impute, MAKE_CHUNKS.out.ch_chunks)
                     ch_versions = ch_versions.mix(IMPUTE_QUILT.out.versions)
 
                     // Add to output channel