Merge pull request #434 from genomic-medicine-sweden/develop

chore: dev to master
genomic-medicine-sweden · Mar 18, 2024 · 9499106 · 9499106
2 parents 7c3a85d + a632bc2
commit 9499106
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diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
@@ -21,9 +21,6 @@ jobs:
         uses: actions/setup-python@v3
         with:
           python-version: 3.8
-      - name: Add conda to system path
-        run: |
-          echo $CONDA/bin >> $GITHUB_PATH
       - name: Install requirements.txt
         run: |
           pip install -r requirements.txt

diff --git a/.tests/jenkins/test_input_main.tsv b/.tests/jenkins/test_input_main.tsv
@@ -55,10 +55,10 @@ results/dna/HD832_T/additional_files/qc/HD832_T.duplication_metrics.txt	20cd0962
 results/dna/HD832_T/additional_files/qc/HD832_T.HsMetrics.txt	79cf2be8375dad0756215acad71f0213
 results/dna/HD832_T/additional_files/qc/HD832_T.insert_size_metrics.txt	68ffcb20c8001106382db7a416eb3c20
 results/dna/HD832_T/additional_files/qc/HD832_T.samtools-stats.txt	d0e806af618b04dd00fe231aa940d6d8
-results/dna/HD832_T/additional_files/vcf/gatk_mutect2_HD832_T.vcf.gz	19dabbf830c8ab2c3d2fc8d635c57294
+results/dna/HD832_T/additional_files/vcf/gatk_mutect2_HD832_T.vcf.gz	5d31eea2b62d5acfc17cdcdd4fbc1e2f
 results/dna/HD832_T/additional_files/vcf/HD832_T.annotated.exon_only.filter.hard_filter.vcf	28abf525563712c6c8755d6842f5f59c
 results/dna/HD832_T/additional_files/vcf/HD832_T.annotated.exon_only.filter.soft_filter.vcf	1ded59457be545896d374024b39c0cd0
-results/dna/HD832_T/additional_files/vcf/HD832_T.annotated.vcf.gz	32774b265215ef84447fc598c3477fae
+results/dna/HD832_T/additional_files/vcf/HD832_T.annotated.vcf.gz	919a2d85ed3a86169772c530ae0e4902
 results/dna/HD832_T/additional_files/vcf/vardict_HD832_T.vcf.gz	e105f2145cd7ee18b0912f696ecc86bb
 results/dna/HD832_T/biomarker/HD832_T.msisensor_pro.score.tsv	ec30212327f70eea52bf123bf8a5b6d2
 results/dna/HD832_T/biomarker/HD832_T.pathology_purecn.scarhrd_cnvkit_score.txt	4b722d55d746bd2b1cc8699ebd97f2ce
@@ -87,10 +87,10 @@ results/dna/NA12878_T/additional_files/qc/NA12878_T.duplication_metrics.txt	355b
 results/dna/NA12878_T/additional_files/qc/NA12878_T.HsMetrics.txt	413cd12525229fd92e1466c6807e1b6d
 results/dna/NA12878_T/additional_files/qc/NA12878_T.insert_size_metrics.txt	c0e59b052483e816bf73b27a8f1acf6e
 results/dna/NA12878_T/additional_files/qc/NA12878_T.samtools-stats.txt	f46d29555a2159425965938cbd0569f7
-results/dna/NA12878_T/additional_files/vcf/gatk_mutect2_NA12878_T.vcf.gz	d171e96a8d0a654bad5ac54968a80796
+results/dna/NA12878_T/additional_files/vcf/gatk_mutect2_NA12878_T.vcf.gz	2bb3ba66ec6bc9bc8d6740f3b4dab3b4
 results/dna/NA12878_T/additional_files/vcf/NA12878_T.annotated.exon_only.filter.hard_filter.vcf	abb4aad15483118c2c04b6b54ff21f5b
-results/dna/NA12878_T/additional_files/vcf/NA12878_T.annotated.exon_only.filter.soft_filter.vcf	af9ff932307ac0a63f863a560d655149
-results/dna/NA12878_T/additional_files/vcf/NA12878_T.annotated.vcf.gz	d1ed6519626ffe7daae5370f1767eedb
+results/dna/NA12878_T/additional_files/vcf/NA12878_T.annotated.exon_only.filter.soft_filter.vcf	238e5a6dc8f59134a7a4e5132c3a393e
+results/dna/NA12878_T/additional_files/vcf/NA12878_T.annotated.vcf.gz	a1f621cfbbb61723685ab7acd26bf25b
 results/dna/NA12878_T/additional_files/vcf/vardict_NA12878_T.vcf.gz	d4b82ab064afe007f46af1da81027101
 results/dna/NA12878_T/biomarker/NA12878_T.msisensor_pro.score.tsv	c6d1341e7c112a01e1dba61e460167ac
 results/dna/NA12878_T/biomarker/NA12878_T.pathology_purecn.scarhrd_cnvkit_score.txt	e98b73e2b3f15616a50c4f494f8493b2
@@ -119,7 +119,7 @@ results/dna/VAL2022_T/additional_files/qc/VAL2022_T.duplication_metrics.txt	3161
 results/dna/VAL2022_T/additional_files/qc/VAL2022_T.HsMetrics.txt	678188a31cb794a729b70c7a84ece6eb
 results/dna/VAL2022_T/additional_files/qc/VAL2022_T.insert_size_metrics.txt	e0e354ef710a189bbb910cc2558d1431
 results/dna/VAL2022_T/additional_files/qc/VAL2022_T.samtools-stats.txt	fcdedb544ce58edf94d76a0bc36171e3
-results/dna/VAL2022_T/additional_files/vcf/gatk_mutect2_VAL2022_T.vcf.gz	ce3cd8a94b0d4f56a7e93a1a313d9b49
+results/dna/VAL2022_T/additional_files/vcf/gatk_mutect2_VAL2022_T.vcf.gz	c7e1498a6df9f218b4ac3b32ffad1a84
 results/dna/VAL2022_T/additional_files/vcf/VAL2022_T.annotated.exon_only.filter.hard_filter.vcf	1cb3c5f2d244f43e36d57a95e0dcafaa
 results/dna/VAL2022_T/additional_files/vcf/VAL2022_T.annotated.exon_only.filter.soft_filter.vcf	0f7f935ad35f3ffb1d59db09fc1407a3
 results/dna/VAL2022_T/additional_files/vcf/VAL2022_T.annotated.vcf.gz	d539a550debe1c111428e9035242c28b

diff --git a/requirements.txt b/requirements.txt
@@ -5,7 +5,6 @@ singularity==3.0.0
 jinja2==3.0.1
 networkx
 drmaa
-cyvcf2==0.30.16
 tabulate<0.9.0
 pulp<2.8
 smart_open<7.0.0
diff --git a/workflow/env/copy_result.yaml b/workflow/env/copy_result.yaml
diff --git a/workflow/envs/bcftools.yaml b/workflow/envs/bcftools.yaml
diff --git a/workflow/envs/call_small_cnv_deletions.yaml b/workflow/envs/call_small_cnv_deletions.yaml
diff --git a/workflow/envs/cnv_html_report.yaml b/workflow/envs/cnv_html_report.yaml
diff --git a/workflow/envs/cnv_json.yaml b/workflow/envs/cnv_json.yaml
diff --git a/workflow/envs/cnv_tsv_report.yaml b/workflow/envs/cnv_tsv_report.yaml
diff --git a/workflow/envs/exon_skipping.yaml b/workflow/envs/exon_skipping.yaml
diff --git a/workflow/envs/fix_vcf_ad_for_qci.yaml b/workflow/envs/fix_vcf_ad_for_qci.yaml
diff --git a/workflow/envs/hotspot_info.yaml b/workflow/envs/hotspot_info.yaml
diff --git a/workflow/envs/hotspot_report.yaml b/workflow/envs/hotspot_report.yaml
diff --git a/workflow/envs/house_keeping_gene_coverage.yaml b/workflow/envs/house_keeping_gene_coverage.yaml
diff --git a/workflow/envs/merge_json.yaml b/workflow/envs/merge_json.yaml
diff --git a/workflow/envs/report_fusions.yaml b/workflow/envs/report_fusions.yaml
diff --git a/workflow/envs/report_gene_fuse.yaml b/workflow/envs/report_gene_fuse.yaml
diff --git a/workflow/rules/call_small_cnv_amplifications.smk b/workflow/rules/call_small_cnv_amplifications.smk
@@ -31,8 +31,6 @@ rule call_small_cnv_amplifications:
         time=config.get("call_small_cnv_amplifications", {}).get("time", config["default_resources"]["time"]),
     container:
         config.get("call_small_cnv_amplifications", {}).get("container", config["default_container"])
-    conda:
-        "../envs/call_small_cnv_deletions.yaml"
     message:
         "{rule}: call small amplifications in cnv data into {output.amplifications}"
     script:

diff --git a/workflow/rules/call_small_cnv_deletions.smk b/workflow/rules/call_small_cnv_deletions.smk
@@ -31,8 +31,6 @@ rule call_small_cnv_deletions:
         time=config.get("call_small_cnv_deletions", {}).get("time", config["default_resources"]["time"]),
     container:
         config.get("call_small_cnv_deletions", {}).get("container", config["default_container"])
-    conda:
-        "../envs/call_small_cnv_deletions.yaml"
     message:
         "{rule}: call small deletions in cnv data into {output.deletions}"
     script:

diff --git a/workflow/rules/cnv_tsv_report.smk b/workflow/rules/cnv_tsv_report.smk
@@ -41,8 +41,6 @@ rule cnv_tsv_report:
         time=config.get("cnv_tsv_report", {}).get("time", config["default_resources"]["time"]),
     container:
         config.get("cnv_tsv_report", {}).get("container", config["default_container"])
-    conda:
-        "../envs/cnv_tsv_report.yaml"
     message:
         "{rule}: Convert cnv vcf to a tsv file: {output.tsv}"
     script:

diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -235,7 +235,6 @@ def generate_copy_code(workflow, output_spec):
         code += f'@workflow.output("{output_file}")\n'
         code += f'@workflow.log("logs/{rule_name}_{result_file}.log")\n'
         code += f'@workflow.container("{copy_container}")\n'
-        code += f'@workflow.conda("../env/copy_result.yaml")\n'
         code += f'@workflow.resources(time = "{time}", threads = {threads}, mem_mb = {mem_mb}, mem_per_cpu = {mem_per_cpu}, partition = "{partition}")\n'
         code += '@workflow.shellcmd("cp --preserve=timestamps {input} {output}")\n\n'
         code += "@workflow.run\n"
@@ -244,7 +243,6 @@ def generate_copy_code(workflow, output_spec):
             "conda_env, container_img, singularity_args, use_singularity, env_modules, bench_record, jobid, is_shell, "
             "bench_iteration, cleanup_scripts, shadow_dir, edit_notebook, conda_base_path, basedir, runtime_sourcecache_path, "
             "__is_snakemake_rule_func=True):\n"
-            '\tshell ( "(cp {input[0]} {output[0]}) &> {log}" , bench_record=bench_record, bench_iteration=bench_iteration)\n\n'
             '\tshell ( "(cp --preserve=timestamps {input[0]} {output[0]}) &> {log}" , bench_record=bench_record, bench_iteration=bench_iteration)\n\n'
         )
 

diff --git a/workflow/rules/common_references.smk b/workflow/rules/common_references.smk
@@ -96,7 +96,6 @@ def generate_copy_code(workflow, output_spec):
         code += f'@workflow.output("{output_file}")\n'
         code += f'@workflow.log("logs/{rule_name}_{result_file}.log")\n'
         code += f'@workflow.container("{copy_container}")\n'
-        code += f'@workflow.conda("../env/copy_result.yaml")\n'
         code += f'@workflow.resources(time = "{time}", threads = {threads}, mem_mb = {mem_mb}, mem_per_cpu = {mem_per_cpu}, partition = "{partition}")\n'
         code += '@workflow.shellcmd("cp --preserve=timestamps {input} {output}")\n\n'
         code += "@workflow.run\n"
@@ -105,7 +104,6 @@ def generate_copy_code(workflow, output_spec):
             "conda_env, container_img, singularity_args, use_singularity, env_modules, bench_record, jobid, is_shell, "
             "bench_iteration, cleanup_scripts, shadow_dir, edit_notebook, conda_base_path, basedir, runtime_sourcecache_path, "
             "__is_snakemake_rule_func=True):\n"
-            '\tshell ( "(cp {input[0]} {output[0]}) &> {log}" , bench_record=bench_record, bench_iteration=bench_iteration)\n\n'
             '\tshell ( "(cp --preserve=timestamps {input[0]} {output[0]}) &> {log}" , bench_record=bench_record, bench_iteration=bench_iteration)\n\n'
         )
 

diff --git a/workflow/rules/exon_skipping.smk b/workflow/rules/exon_skipping.smk
@@ -26,8 +26,6 @@ rule exon_skipping:
         time=config.get("exon_skipping", {}).get("time", config["default_resources"]["time"]),
     container:
         config.get("exon_skipping", {}).get("container", config["default_container"])
-    conda:
-        "../envs/exon_skipping.yaml"
     message:
         "{rule}: Find intergenic fusions and report them in {output.result}"
     script:

diff --git a/workflow/rules/fix_vcf_ad_for_qci.smk b/workflow/rules/fix_vcf_ad_for_qci.smk
@@ -25,8 +25,6 @@ rule fix_vcf_ad_for_qci:
         time=config.get("fix_vcf_ad_for_qci", {}).get("time", config["default_resources"]["time"]),
     container:
         config.get("fix_vcf_ad_for_qci", {}).get("container", config["default_container"])
-    conda:
-        "../envs/fix_vcf_ad_for_qci.yaml"
     message:
         "{rule}: Correct AD so the correct AF is shown in QCI for vcf {input.vcf}"
     script:

diff --git a/workflow/rules/hotspot_info.smk b/workflow/rules/hotspot_info.smk
@@ -37,8 +37,6 @@ rule hotspot_info:
             "qc/hotspot_info/{sample}_{type}.fastq.gz.fastp_trimming.benchmark.tsv",
             config.get("hotspot_info", {}).get("benchmark_repeats", 1),
         )
-    conda:
-        "../envs/hotspot_info.yaml"
     container:
         config.get("hotspot_info", {}).get("container", config["default_container"])
     message:

diff --git a/workflow/rules/hotspot_report.smk b/workflow/rules/hotspot_report.smk
@@ -39,8 +39,6 @@ rule hotspot_report:
         time=config.get("hotspot_report", {}).get("time", config["default_resources"]["time"]),
     container:
         config.get("hotspot_report", {}).get("container", config["default_container"])
-    conda:
-        "../envs/hotspot_report.yaml"
     message:
         "{rule}: Do stuff on twist_dna_solid_uppsala/{rule}/{wildcards.sample}_{wildcards.type}.input"
     script:

diff --git a/workflow/rules/house_keeping_gene_coverage.smk b/workflow/rules/house_keeping_gene_coverage.smk
@@ -27,8 +27,6 @@ rule house_keeping_gene_coverage:
         time=config.get("house_keeping_gene_coverage", {}).get("time", config["default_resources"]["time"]),
     container:
         config.get("house_keeping_gene_coverage", {}).get("container", config["default_container"])
-    conda:
-        "../envs/house_keeping_gene_coverage.yaml"
     message:
         "{rule}: Find intergenic fusions and report them in {output.result}"
     script: