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Merged
danielnachun merged 2 commits into from
Nov 8, 2026
Merged

Pass cTWAS weight paths to ctwas_assemble.R through a list file #1436

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3ced253
Pass cTWAS weight paths to ctwas_assemble.R through a list file
jaempawi Nov 6, 2026
395302a
fix other file manifest issues
danielnachun Nov 8, 2026
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4 changes: 3 additions & 1 deletion code/SoS/data_preprocessing/genotype/genotype_formatting.ipynb
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Expand Up @@ -1172,9 +1172,11 @@
"output: out\n",
"task: trunk_workers = 1, trunk_size = job_size, walltime = walltime, mem = mem, cores = numThreads, tags = f'{step_name}_{_output:bn}'\n",
"bash: expand= \"${ }\", stderr = f'{_output:n}.stderr', stdout = f'{_output:n}.stdout'\n",
" # The paths go in a file: a genome-wide region list is too long for one command-line argument.\n",
" printf '%s\\n' ${_input:r} > \"${_output:n}.data_files.txt\"\n",
" Rscript ${modular_script_dir}/data_preprocessing/genotype/genotype_formatting.R \\\n",
" --step write_data_list \\\n",
" --data-files \"${\"::\".join([str(x) for x in _input])}\" \\\n",
" --data-files-list \"${_output:n}.data_files.txt\" \\\n",
" --ext \"${ext}\" \\\n",
" --output \"${_output}\" \\\n",
" --numThreads ${numThreads}"
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4 changes: 3 additions & 1 deletion code/SoS/data_preprocessing/phenotype/phenotype_formatting.ipynb
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Expand Up @@ -611,9 +611,11 @@
"input: group_by = \"all\"\n",
"output: f'{cwd}/{name}.{step_name[:-2]}_files.txt'\n",
"bash: expand= \"${ }\", stderr = f'{_output:n}.stderr', stdout = f'{_output:n}.stdout', container = container, entrypoint = entrypoint\n",
" # The paths go in a file: a genome-wide region list is too long for the command line.\n",
" printf '%s\\n' ${_input:r} > \"${_output:n}.inputs.txt\"\n",
" Rscript ${modular_script_dir}/data_preprocessing/phenotype/phenotype_formatting.R --step phenotype_by_region_2 \\\n",
" --cwd \"${cwd}\" \\\n",
" --inputs ${_input} \\\n",
" --inputs-list \"${_output:n}.inputs.txt\" \\\n",
" --output \"${_output}\""
]
},
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4 changes: 3 additions & 1 deletion code/SoS/mnm_analysis/mnm_methods/colocboost.ipynb
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Expand Up @@ -497,7 +497,9 @@
"parameter: ld_meta_data = path()\n",
"# Optional region list whose LAST column lists region/gene IDs to analyze.\n",
"parameter: region_list = path()\n",
"# Region/gene IDs to analyze (space separated on the CLI).\n",
"# Region/gene IDs to analyze (space separated on the CLI). For thousands of IDs\n",
"# use --region-list instead: the IDs reach colocboost_manifest.R as one\n",
"# comma-joined argument, which Linux caps at 128 KiB.\n",
"parameter: region_name = []\n",
"# Optional per-gene association windows (BED: #chr start end ID) overriding the\n",
"# default cis_window for the GWAS extraction window.\n",
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132 changes: 91 additions & 41 deletions code/SoS/mnm_analysis/mnm_methods/mnm_regression.ipynb
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34 changes: 22 additions & 12 deletions code/SoS/mnm_analysis/mnm_postprocessing.ipynb
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Expand Up @@ -97,7 +97,7 @@
"\n",
"The remaining workflows take these additional flags:\n",
"\n",
"- `--tsv_path output_postproc/*.lbf.tsv` (per-region LBF tables to concatenate; `susie_tsv_collapse`)\n",
"- `--tsv_path 'output_postproc/*.lbf.tsv'` (per-region LBF tables to concatenate; `susie_tsv_collapse`. Quote the wildcard so SoS expands it: expanded by the shell, a genome-wide set of files is too long for the command line.)\n",
"- `--annot_tibble <annotation_tibble.tsv>` (annotation tibble used to label variants; `susie_pip_landscape_plot` and `fsusie_extract_effect`)\n",
"- `--trait_to_select 1` (how many traits the credible-set UpSet diagram shows; `susie_upsetR_cs_plot`)\n",
"- `--SNP_list <variant_list.txt>` (variants to annotate; `tmp_annotatation_of_snps`)\n",
Expand Down Expand Up @@ -264,7 +264,7 @@
"source": [
"sos run pipeline/mnm_postprocessing.ipynb susie_tsv_collapse \\\n",
" --cwd output_postproc --study <study_name> \\\n",
" --tsv_path output_postproc/*.lbf.tsv \\\n",
" --tsv_path 'output_postproc/*.lbf.tsv' \\\n",
" --container '' -j1"
]
},
Expand All @@ -276,7 +276,7 @@
},
"source": [
"### Diagnostic plots\n",
"`susie_pip_landscape_plot` draws the PIP landscape; `susie_upsetR_plot` and `susie_upsetR_cs_plot` draw UpSet diagrams of credible-set overlap. The landscape plot needs an annotation tibble; `--trait_to_select` picks how many traits the credible-set diagram shows."
"`susie_pip_landscape_plot` draws the PIP landscape; `susie_upsetR_plot` and `susie_upsetR_cs_plot` draw UpSet diagrams of credible-set overlap. The landscape plot needs an annotation tibble; `--trait_to_select` picks how many traits the credible-set diagram shows. Quote the `--rds_path` wildcard so SoS expands it: expanded by the shell, a genome-wide set of files is too long for the command line."
]
},
{
Expand All @@ -300,13 +300,13 @@
"source": [
"sos run pipeline/mnm_postprocessing.ipynb susie_pip_landscape_plot \\\n",
" --cwd output_postproc --study <study_name> \\\n",
" --rds_path <fine_mapping_dir>/*.fine_mapping.rds \\\n",
" --rds_path '<fine_mapping_dir>/*.fine_mapping.rds' \\\n",
" --annot_tibble <annotation_tibble.tsv> \\\n",
" --container '' -j1\n",
"\n",
"sos run pipeline/mnm_postprocessing.ipynb susie_upsetR_cs_plot \\\n",
" --cwd output_postproc --study <study_name> \\\n",
" --rds_path <fine_mapping_dir>/*.fine_mapping.rds \\\n",
" --rds_path '<fine_mapping_dir>/*.fine_mapping.rds' \\\n",
" --trait_to_select 1 \\\n",
" --container '' -j1"
]
Expand Down Expand Up @@ -1098,8 +1098,10 @@
"output: f'{cwd}/{name}.UpSetR.pdf'\n",
"task: trunk_workers = 1, trunk_size = job_size, walltime = walltime, mem = mem, cores = numThreads, tags = f'{step_name}_{_output:bn}'\n",
"bash: expand = '${ }', stdout = f\"{_output:n}.stdout\", stderr = f\"{_output:n}.stderr\", container = container, entrypoint = entrypoint\n",
" # The paths go in a file: a genome-wide list is too long for the command line.\n",
" printf '%s\\n' ${_input:r} > \"${_output:n}.input.txt\"\n",
" Rscript ${modular_script_dir}/pecotmr_integration/fine_mapping_upset.R \\\n",
" --input ${\" \".join([str(x) for x in _input])} \\\n",
" --input-list \"${_output:n}.input.txt\" \\\n",
" --output ${_output}\n"
]
},
Expand All @@ -1123,8 +1125,10 @@
"output: f'{cwd}/{name}.UpSetR_cs.pdf'\n",
"task: trunk_workers = 1, trunk_size = job_size, walltime = walltime, mem = mem, cores = numThreads, tags = f'{step_name}_{_output:bn}'\n",
"bash: expand = '${ }', stdout = f\"{_output:n}.stdout\", stderr = f\"{_output:n}.stderr\", container = container, entrypoint = entrypoint\n",
" # The paths go in a file: a genome-wide list is too long for the command line.\n",
" printf '%s\\n' ${_input:r} > \"${_output:n}.input.txt\"\n",
" Rscript ${modular_script_dir}/pecotmr_integration/fine_mapping_upset.R \\\n",
" --input ${\" \".join([str(x) for x in _input])} \\\n",
" --input-list \"${_output:n}.input.txt\" \\\n",
" --output ${_output}\n"
]
},
Expand Down Expand Up @@ -1505,8 +1509,10 @@
"task: trunk_workers = 1, walltime = '1h', trunk_size = 1, mem = '16G', cores = 1, tags = f'{_output:bn}'\n",
"bash: expand = \"${ }\", container = container, stderr = f'{_output:n}.stderr', stdout = f'{_output:n}.stdout'\n",
" if [ -e \"${_output:ad}/${name}_cache/\" ]; then\n",
" sed 's/^chr/#chr/' `ls ${_output:ad}/${name}_cache/*tsv |head -n1` | head -n 1 > ${_output:an}.temp\n",
" tail -n +2 -q ${_output:ad}/${name}_cache/*.tsv >> ${_output:an}.temp\n",
" # find + xargs, not a glob: a genome-wide run has one cache table per region, too many for one command line.\n",
" first_table=$(find \"${_output:ad}/${name}_cache/\" -maxdepth 1 -type f -name '*tsv' | sort | head -n 1)\n",
" sed 's/^chr/#chr/' \"$first_table\" | head -n 1 > ${_output:an}.temp\n",
" find \"${_output:ad}/${name}_cache/\" -maxdepth 1 -type f -name '*.tsv' -print0 | sort -z | xargs -0 -r tail -n +2 -q >> ${_output:an}.temp\n",
" error_files=$(find \"${_output:ad}/${name}_cache/\" -type f -name \"*_error\")\n",
"\n",
" if [[ -n $error_files ]]; then\n",
Expand Down Expand Up @@ -1625,8 +1631,10 @@
"parameter: remove_cache = False\n",
"output: f\"{cache_path:d}/{output_file}\" \n",
"bash: expand = \"${ }\", container = container, stderr = f'{_input:n}.stderr', stdout = f'{_input:n}.stdout' \n",
" head -n 1 -q ${cache_path}/*.tsv | sed 's/^chr/#chr/' | head -n 1 > ${_output}\n",
" tail -n +2 -q ${cache_path}/*.tsv >> ${_output}\n",
" # find + xargs, not a glob: one cache table per region is too many for one command line.\n",
" first_table=$(find \"${cache_path}\" -maxdepth 1 -type f -name '*.tsv' | sort | head -n 1)\n",
" head -n 1 \"$first_table\" | sed 's/^chr/#chr/' > ${_output}\n",
" find \"${cache_path}\" -maxdepth 1 -type f -name '*.tsv' -print0 | sort -z | xargs -0 -r tail -n +2 -q >> ${_output}\n",
" if ${\"true\" if remove_cache else \"false\"}; then\n",
" rm -rf ${cache_path}\n",
" fi"
Expand Down Expand Up @@ -1708,8 +1716,10 @@
"output: f\"{cwd}/summary/{name}.{qtl_type}{_tag}.top_loci.bed.gz\"\n",
"task: trunk_workers = 1, walltime = '2h', trunk_size = 1, mem = '8G', cores = 1, tags = f'{_output:bn}'\n",
"bash: expand = \"${ }\", container = container, stderr = f'{_output:n}.stderr', stdout = f'{_output:n}.stdout', entrypoint=entrypoint\n",
" # The paths go in a file: a genome-wide list is too long for the command line.\n",
" printf '%s\\n' ${_input:r} > \"${_output:nn}.input.txt\"\n",
" Rscript ${modular_script_dir}/pecotmr_integration/fine_mapping_bed_merge.R \\\n",
" --input ${_input:r} \\\n",
" --input-list \"${_output:nn}.input.txt\" \\\n",
" --output ${_output:r}"
]
},
Expand Down
5 changes: 4 additions & 1 deletion code/SoS/molecular_phenotypes/QC/splicing_normalization.ipynb
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Expand Up @@ -554,7 +554,10 @@
"output: f'{cwd}/{leafcutter_version}/{dataset}_intron_usage_perind.junc'\n",
"bash: container=container, expand= \"${ }\", stderr = f'{_output[0]:n}.stderr', stdout = f'{_output[0]:n}.stderr' \n",
" cd ${cwd}\n",
" realpath ${junc_path}/*${file_suffix} > ${_output}.tmp\n",
" # find, not a glob: a cohort's junction files are too many arguments for\n",
" # realpath. Hidden files are skipped, as the glob skipped them.\n",
" find \"${junc_path}/\" -mindepth 1 -maxdepth 1 -name \"*${file_suffix}\" ! -name '.*' -print0 \\\n",
" | sort -z | xargs -0 -r realpath > ${_output}.tmp\n",
" grep -v \"all\" ${_output}.tmp > ${_output}\n",
" rm ${_output}.tmp"
]
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16 changes: 12 additions & 4 deletions code/SoS/molecular_phenotypes/calling/RNA_calling.ipynb
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Expand Up @@ -954,11 +954,13 @@
"input: group_by = \"all\"\n",
"output: f'{cwd}/{sample_list:n}.trimmed.txt'\n",
"bash: expand = \"${ }\", stderr = f'{_output:n}.stderr', stdout = f'{_output:n}.stdout'\n",
" # The paths go in a file: a large cohort's list is too long for the command line.\n",
" printf '%s\\n' ${_input:r} > \"${_output:n}.input.txt\"\n",
" Rscript ${modular_script_dir}/molecular_phenotypes/calling/RNA_calling.R \\\n",
" --step fastp_manifest \\\n",
" --sample-list \"${sample_list}\" \\\n",
" --is-paired-end ${is_paired_end} \\\n",
" --input ${' '.join([f'\"{x}\"' for x in _input])} \\\n",
" --input-list \"${_output:n}.input.txt\" \\\n",
" --output \"${_output}\"\n"
]
},
Expand Down Expand Up @@ -1255,10 +1257,12 @@
"output: f'{cwd}/{sample_list:bn}.bam_file_list'\n",
"task: trunk_workers = 1, trunk_size = 1, walltime = walltime, mem = mem, cores = 1\n",
"bash: expand= \"${ }\", stderr = f'{_output:n}.stderr', stdout = f'{_output:n}.stdout'\n",
" # The paths go in a file: a large cohort's list is too long for the command line.\n",
" printf '%s\\n' ${_input:r} > \"${_output}.input.txt\"\n",
" Rscript ${modular_script_dir}/molecular_phenotypes/calling/RNA_calling.R \\\n",
" --step star_align_3 \\\n",
" --output \"${_output}\" \\\n",
" --input ${\" \".join([str(x) for x in _input])} \\\n",
" --input-list \"${_output}.input.txt\" \\\n",
" --sample-id ${\" \".join([str(x) for x in sample_id])} \\\n",
" --strand ${\" \".join([str(x) for x in strand])} \\\n",
" --var-vcf-file \"${varVCFfile}\"\n"
Expand Down Expand Up @@ -1360,11 +1364,13 @@
" f'{cwd}/{bam_list:bn}.rnaseqc.metrics.tsv'\n",
"task: trunk_workers = 1, trunk_size = job_size, walltime = walltime, mem = mem, cores = numThreads\n",
"bash: expand= \"${ }\", stderr = f'{_output[0]:n}.stderr', stdout = f'{_output[0]:n}.stdout'\n",
" # The paths go in a file: a large cohort's list is too long for the command line.\n",
" printf '%s\\n' ${_input:r} > \"${cwd}/${bam_list:bn}.rnaseqc.input.txt\"\n",
" Rscript ${modular_script_dir}/molecular_phenotypes/calling/RNA_calling.R \\\n",
" --step rnaseqc_merge \\\n",
" --cwd \"${cwd}\" \\\n",
" --name \"${bam_list:bn}\" \\\n",
" --input ${\" \".join([str(x) for x in _input])}\n"
" --input-list \"${cwd}/${bam_list:bn}.rnaseqc.input.txt\"\n"
]
},
{
Expand Down Expand Up @@ -1457,11 +1463,13 @@
"\n",
"task: trunk_workers = 1, walltime = walltime, mem = mem, cores = numThreads, trunk_size = job_size\n",
"bash: expand= \"${ }\", stderr = f'{_output[0]:n}.stderr', stdout = f'{_output[0]:n}.stdout'\n",
" # The paths go in a file: a large cohort's list is too long for the command line.\n",
" printf '%s\\n' ${_input:r} > \"${cwd}/${bam_list:bn}.rsem.input.txt\"\n",
" Rscript ${modular_script_dir}/molecular_phenotypes/calling/RNA_calling.R \\\n",
" --step rsem_call_2 \\\n",
" --cwd \"${cwd}\" \\\n",
" --name \"${bam_list:bn}\" \\\n",
" --input ${\" \".join([str(x) for x in _input])}\n"
" --input-list \"${cwd}/${bam_list:bn}.rsem.input.txt\"\n"
]
},
{
Expand Down
12 changes: 9 additions & 3 deletions code/SoS/multivariate_genome/MASH/mash_posterior.ipynb
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Expand Up @@ -764,8 +764,10 @@
"input: group_by = \"all\"\n",
"output: f\"{cwd}/{name}.posterior_sum.csv\"\n",
"bash: expand = \"${ }\", stderr = f'{_output:n}.stderr', stdout = f'{_output:n}.stdout', container = container\n",
" # The paths go in a file: a genome-wide list is too long for the command line.\n",
" printf '%s\\n' ${_input:r} > \"${_output:n}.contrast.txt\"\n",
" Rscript ${modular_script_dir}/pecotmr_integration/mash_posterior_contrast_summary.R \\\n",
" --contrast ${_input} \\\n",
" --contrast-list \"${_output:n}.contrast.txt\" \\\n",
" --cells ${','.join(cells)} \\\n",
" --p-cutoff ${p_cut} \\\n",
" --output ${_output}"
Expand Down Expand Up @@ -886,8 +888,10 @@
"input: group_by = \"all\"\n",
"output: f\"{cwd}/{name}.{step_name}.feature_score_sum.csv\"\n",
"bash: expand = \"${ }\", stderr = f'{_output:n}.stderr', stdout = f'{_output:n}.stdout', container = container\n",
" # The paths go in a file: a genome-wide list is too long for the command line.\n",
" printf '%s\\n' ${_input:r} > \"${_output:n}.scores.txt\"\n",
" Rscript ${modular_script_dir}/pecotmr_integration/mash_feature_score_merge.R \\\n",
" --scores ${_input} \\\n",
" --scores-list \"${_output:n}.scores.txt\" \\\n",
" --output ${_output}"
]
},
Expand Down Expand Up @@ -983,8 +987,10 @@
"input: group_by = \"all\"\n",
"output: f\"{cwd}/{name}.{step_name}.feature_score_sum.csv\"\n",
"bash: expand = \"${ }\", stderr = f'{_output:n}.stderr', stdout = f'{_output:n}.stdout', container = container\n",
" # The paths go in a file: a genome-wide list is too long for the command line.\n",
" printf '%s\\n' ${_input:r} > \"${_output:n}.scores.txt\"\n",
" Rscript ${modular_script_dir}/pecotmr_integration/mash_feature_score_merge.R \\\n",
" --scores ${_input} \\\n",
" --scores-list \"${_output:n}.scores.txt\" \\\n",
" --output ${_output}"
]
}
Expand Down
13 changes: 9 additions & 4 deletions code/SoS/multivariate_genome/MASH/mash_preprocessing.ipynb
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Expand Up @@ -538,14 +538,17 @@
"with open(fine_mapping_meta) as _f:\n",
" _rows = list(csv.DictReader(_f, delimiter = '\\t'))\n",
"_fmr_paths = [r[finemapping_column] for r in _rows]\n",
"_region_ids = \",\".join(str(r[region_column]) for r in _rows)\n",
"_region_ids = [str(r[region_column]) for r in _rows]\n",
"input: _fmr_paths\n",
"output: f\"{cwd}/{name}.mash_input.rds\"\n",
"task: trunk_workers = 1, trunk_size = job_size, walltime = walltime, mem = mem, cores = numThreads, tags = f'{step_name}_{_output:bn}'\n",
"bash: expand = \"${ }\", stderr = f'{_output:n}.stderr', stdout = f'{_output:n}.stdout', container = container\n",
" # The paths and region ids go in files: genome-wide lists are too long for the command line.\n",
" printf '%s\\n' ${_input:r} > \"${_output:n}.objects.txt\"\n",
" printf '%s\\n' ${\" \".join(repr(x) for x in _region_ids)} > \"${_output:n}.region_ids.txt\"\n",
" Rscript ${modular_script_dir}/pecotmr_integration/mash_preprocessing.R \\\n",
" --objects ${_input} \\\n",
" --region-ids ${_region_ids} \\\n",
" --objects-list \"${_output:n}.objects.txt\" \\\n",
" --region-ids-list \"${_output:n}.region_ids.txt\" \\\n",
" --coverage ${coverage} \\\n",
" --n-random ${n_random} \\\n",
" --n-null ${n_null} \\\n",
Expand Down Expand Up @@ -622,8 +625,10 @@
"output: f\"{cwd}/{name}.mash_input.rds\"\n",
"task: trunk_workers = 1, trunk_size = job_size, walltime = walltime, mem = mem, cores = numThreads, tags = f'{_output:bn}'\n",
"bash: expand = \"${ }\", stderr = f'{_output:n}.stderr', stdout = f'{_output:n}.stdout', container = container\n",
" # The paths go in a file: a genome-wide list is too long for the command line.\n",
" printf '%s\\n' ${_input:r} > \"${_output:n}.objects.txt\"\n",
" Rscript ${modular_script_dir}/pecotmr_integration/mash_preprocessing.R \\\n",
" --objects ${_input} \\\n",
" --objects-list \"${_output:n}.objects.txt\" \\\n",
" --n-random ${n_random} \\\n",
" --n-null ${n_null} \\\n",
" --exclude-condition \"${','.join(exclude_condition)}\" \\\n",
Expand Down
9 changes: 7 additions & 2 deletions code/SoS/pecotmr_integration/SuSiE_enloc.ipynb
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Expand Up @@ -435,6 +435,8 @@
"parameter: region_list = path()\n",
"# Optional: if a region name is provided \n",
"# the analysis would be focused on the union of provides region list and region names\n",
"# For thousands of regions use --region-list instead: the names reach\n",
"# enloc_manifest.R as one comma-joined argument, which Linux caps at 128 KiB.\n",
"parameter: region_name = []\n",
"# It is required to input the name of the analysis\n",
"parameter: name = f\"{xqtl_meta_data:bnn}.{gwas_meta_data:bnn}\"\n",
Expand Down Expand Up @@ -571,9 +573,12 @@
" # The xQTL and GWAS sides are already S4 FineMappingResult collections\n",
" # (fine_mapping output); qtl_enrichment.R combines its multi-file inputs\n",
" # itself, so the legacy legacy_enloc_finemap_convert.R step is gone.\n",
" # The paths go in files: a condition's genome-wide list is too long for the command line.\n",
" printf '%s\\n' ${_input:r} > \"${_output:n}.qtl_fine_mapping.txt\"\n",
" printf '%s\\n' ${\" \".join(repr(x) for x in _jobs[\"gwas_files\"].split(\",\"))} > \"${_output:n}.gwas_fine_mapping.txt\"\n",
" Rscript ${modular_script_dir}/pecotmr_integration/qtl_enrichment.R \\\n",
" --qtl-fine-mapping ${\" \".join([str(x) for x in _input])} \\\n",
" --gwas-fine-mapping ${_jobs[\"gwas_files\"].replace(\",\", \" \")} \\\n",
" --qtl-fine-mapping-list \"${_output:n}.qtl_fine_mapping.txt\" \\\n",
" --gwas-fine-mapping-list \"${_output:n}.gwas_fine_mapping.txt\" \\\n",
" --ncore ${numThreads} \\\n",
" ${seed_arg} \\\n",
" --output ${_output}\n"
Expand Down
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