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working commit of the fmx-assign-to-gt functionality #44

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c558719
working commit of the fmx-assign-to-gt functionality
erflynn Nov 1, 2023
8eb8cc1
Merge branch 'main' of github.com:UCSF-DSCOLAB/data_processing_pipeli…
erflynn Nov 6, 2023
494714a
moved fmx-assign-to-gt
erflynn Nov 8, 2023
4c7b6c8
added gtcheck run scripts
erflynn Nov 8, 2023
39ed921
fixed separate_fmx bug introduced by deduplicating module
erflynn Nov 9, 2023
a60ac63
Merge branch 'main' of github.com:UCSF-DSCOLAB/data_processing_pipeli…
erflynn Nov 9, 2023
c35249b
moved fmx vcf channels to improve workflow logic
erflynn Dec 8, 2023
c3578d6
Merge branch 'main' of github.com:UCSF-DSCOLAB/data_processing_pipeli…
erflynn Jan 31, 2024
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72 changes: 0 additions & 72 deletions single_cell_RNAseq/bin/process_vcf_map.R
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220 changes: 0 additions & 220 deletions single_cell_RNAseq/bin/vcf-match-sample-ids.pl
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1 change: 1 addition & 0 deletions single_cell_RNAseq/config/container.config
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ params {
cellranger = "${params.container.singularity_dir}/cellranger/6.0.2/cellranger.sif"
popscle = "${params.container.singularity_dir}/popscle/da70fc78da385ef049e0e890342acfd62842cae0/popscle.sif"
rsinglecell = "${params.container.singularity_dir}/RSingleCell/v4/RSingleCell.sif"
rplus_bcftools = "${params.container.singularity_dir}/rplus_bcftools/rsinglecell_bcftools.sif"
python = "${params.container.singularity_dir}/cytof/v3/cytof.sif"
}
}
8 changes: 5 additions & 3 deletions single_cell_RNAseq/example-inputs/param_2.json
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,9 @@
"skip_cellranger": true,
"merge_for_demux" : true,
"merge_demux_dir" : "/krummellab/data1/${USER}/tutorial_lib_sep/freemuxlet_data/",
"demux_method" : "demuxlet",
"demux_method" : "freemuxlet",
"fmx_assign_to_gt": true,
"ref_vcf_dir": "/krummellab/data1/pipeline_test_data/assays/scRNA_seq/modality/gex/downsampled_jurkat_tcell/inputs/variants/",
"run_doubletfinder" : true,
"mincell" : 3,
"minfeature" : 100,
Expand All @@ -19,7 +21,7 @@
{
"name": "DM1",
"nsamples" : "2",
"vcf": "/krummellab/data1/pipeline_test_data/assays/scRNA_seq/modality/gex/downsampled_jurkat_tcell/inputs/variants/jurkat_293t_exons_only_w_chr_hg38.vcf",
"vcf": "jurkat_293t_exons_only_w_chr_hg38.vcf",
"libraries": [
{
"name": "TEST-POOL-DM1-SCG1",
Expand All @@ -35,7 +37,7 @@
},
{
"nsamples": "2",
"vcf": "/krummellab/data1/pipeline_test_data/assays/scRNA_seq/modality/gex/downsampled_jurkat_tcell/inputs/variants/jurkat_293t_exons_only_w_chr_hg38.vcf",
"vcf": "jurkat_293t_exons_only_w_chr_hg38.vcf",
"name": "DM2",
"libraries": [
{
Expand Down
32 changes: 28 additions & 4 deletions single_cell_RNAseq/modules/pipeline_tasks.nf
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Expand Up @@ -285,8 +285,7 @@ process FREEMUXLET_POOL {
publishDir "${params.project_dir}/data/single_cell_GEX/logs/${pool}/", mode: 'copy', pattern: ".command.log", saveAs: { filename -> "freemuxlet.log" }

container "${params.container.popscle}"
containerOptions "-B ${params.ref.fmx_dir}"


input:
tuple val(pool), val(nsamples), path(merged_plp), path(merged_var), path(merged_cel), path(merged_barcodes)

Expand Down Expand Up @@ -315,8 +314,7 @@ process FREEMUXLET_LIBRARY {
publishDir "${params.project_dir}/data/single_cell_GEX/logs/${library}/", mode: 'copy', pattern: ".command.log", saveAs: { filename -> "freemuxlet.log" }

container "${params.container.popscle}"
containerOptions "-B ${params.ref.fmx_dir}"


input:
tuple val(library), val(nsamples), path(plp_files)

Expand All @@ -342,6 +340,32 @@ process FREEMUXLET_LIBRARY {
}


/*
* Run assign to gt for a pool or library
*/
process FMX_ASSIGN_TO_GT {
publishDir "${params.project_dir}/fmx_assign_to_gt/${pool}/", mode: 'copy', pattern: "${pool}_gtcheck*"
publishDir "${params.project_dir}/data/single_cell_GEX/logs/${pool}/", mode: 'copy', pattern: ".command.log", saveAs: { filename -> "fmx_assign_to_gt.log" }

container "${params.container.rplus_bcftools}"
containerOptions "-B ${params.project_dir} -B ${params.settings.ref_vcf_dir}"

input:
tuple val(pool), val(ref_vcf), path(fmx_vcf)

output:
tuple val(pool), path("${pool}*"), emit: outfiles
path(".command.log"), emit: log


"""
bash ${projectDir}/bin/run_gtcheck.sh ${pool} ${params.settings.ref_vcf_dir}/${ref_vcf} ${fmx_vcf}
Rscript ${projectDir}/bin/examine_gtcheck.R ${pool} ${pool}_gtcheck.out
"""

}


/*
* Run demuxlet for a library
*/
Expand Down
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