change the output name of cnv modules

d3b-center · Jul 17, 2023 · 3bde20f · 3bde20f
1 parent 6676cf8
commit 3bde20f
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Showing 16 changed files with 515,811 additions and 247,331 deletions.
diff --git a/analyses/copy_number_consensus_call/README.md b/analyses/copy_number_consensus_call/README.md
diff --git a/analyses/copy_number_consensus_call/Snakefile b/analyses/copy_number_consensus_call/Snakefile
@@ -8,9 +8,9 @@ wildcard_constraints:
 ## Define the first rule of the Snakefile. This rule determines what the final file is and which steps to be taken.
 rule all:
  input:
- "results/cnv_consensus.tsv",
- "results/cnv_neutral.bed",
- "results/cnv-consensus.seg.gz"
+ "results/cnv_consensus-freec-ckit-gatk.tsv",
+ "results/cnv_neutral-freec-ckit-gatk.bed",
+ "results/cnv-consensus-freec-ckit-gatk.seg.gz"
 
 
 scratch_loc = config["scratch"] + '/'
@@ -290,7 +290,7 @@ rule merge_neutral:
  expand(scratch_loc + "endpoints/{sample}.neutral.bed",
  sample = config["samples"])
  output:
- "results/cnv_neutral.bed"
+ "results/cnv_neutral-freec-ckit-gatk.bed"
  shell:
  "cat {input} > {output}"
 
@@ -315,18 +315,18 @@ rule clean_output:
  script=os.path.join(config["scripts"], "remove_dup_NULL_overlap_entries.py"),
  cnv_file = scratch_loc + "endpoints/all_CNVs_combined.tsv"
  output:
- "results/cnv_consensus.tsv"
+ "results/cnv_consensus-freec-ckit-gatk.tsv"
  shell:
  "python3 {input.script} --file {input.cnv_file} > {output}"
 
 rule make_segfile:
  input:
  script= os.path.join(config["scripts"], "bed_to_segfile.R"),
- consensus = "results/cnv_consensus.tsv",
- neutral = "results/cnv_neutral.bed",
+ consensus = "results/cnv_consensus-freec-ckit-gatk.tsv",
+ neutral = "results/cnv_neutral-freec-ckit-gatk.bed",
  uncalled = "results/uncalled_samples.tsv"
  output:
- "results/cnv-consensus.seg.gz"
+ "results/cnv-consensus-freec-ckit-gatk.seg.gz"
  shell:
  "Rscript {input.script}"
  " -i {input.consensus}"

diff --git a/analyses/copy_number_consensus_call/merge_cnv_file.R b/analyses/copy_number_consensus_call/merge_cnv_file.R
diff --git a/...nsensus_call/results/cnv-consensus.seg.gz → ...ults/cnv-consensus-freec-ckit-gatk.seg.gz b/...nsensus_call/results/cnv-consensus.seg.gz → ...ults/cnv-consensus-freec-ckit-gatk.seg.gz
diff --git a/analyses/copy_number_consensus_call/results/cnv-consensus_full.seg.gz b/analyses/copy_number_consensus_call/results/cnv-consensus_full.seg.gz
diff --git a/..._consensus_call/results/cnv_consensus.tsv → ...results/cnv_consensus-freec-ckit-gatk.tsv b/..._consensus_call/results/cnv_consensus.tsv → ...results/cnv_consensus-freec-ckit-gatk.tsv
diff --git a/...er_consensus_call/results/cnv_neutral.bed → ...l/results/cnv_neutral-freec-ckit-gatk.bed b/...er_consensus_call/results/cnv_neutral.bed → ...l/results/cnv_neutral-freec-ckit-gatk.bed
diff --git a/analyses/copy_number_consensus_call_manta/README.md b/analyses/copy_number_consensus_call_manta/README.md
diff --git a/analyses/copy_number_consensus_call_manta/Snakefile b/analyses/copy_number_consensus_call_manta/Snakefile
@@ -8,9 +8,9 @@ wildcard_constraints:
 ## Define the first rule of the Snakefile. This rule determines what the final file is and which steps to be taken.
 rule all:
  input:
- "results/cnv_consensus.tsv",
- "results/cnv_neutral.bed",
- "results/cnv-consensus.seg.gz"
+ "results/cnv_consensus-freec-ckit-manta.tsv",
+ "results/cnv_neutral-freec-ckit-manta.bed",
+ "results/cnv-consensus-freec-ckit-manta.seg.gz"
 
 
 scratch_loc = config["scratch"] + '/'
@@ -287,7 +287,7 @@ rule merge_neutral:
  expand(scratch_loc + "endpoints/{sample}.neutral.bed",
  sample = config["samples"])
  output:
- "results/cnv_neutral.bed"
+ "results/cnv_neutral-freec-ckit-manta.bed"
  shell:
  "cat {input} > {output}"
 
@@ -312,18 +312,18 @@ rule clean_output:
  script=os.path.join(config["scripts"], "remove_dup_NULL_overlap_entries.py"),
  cnv_file = scratch_loc + "endpoints/all_CNVs_combined.tsv"
  output:
- "results/cnv_consensus.tsv"
+ "results/cnv_consensus-freec-ckit-manta.tsv"
  shell:
  "python3 {input.script} --file {input.cnv_file} > {output}"
 
 rule make_segfile:
  input:
  script= os.path.join(config["scripts"], "bed_to_segfile.R"),
- consensus = "results/cnv_consensus.tsv",
- neutral = "results/cnv_neutral.bed",
+ consensus = "results/cnv_consensus-freec-ckit-manta.tsv",
+ neutral = "results/cnv_neutral-freec-ckit-manta.bed",
  uncalled = "results/uncalled_samples.tsv"
  output:
- "results/cnv-consensus.seg.gz"
+ "results/cnv-consensus-freec-ckit-manta.seg.gz"
  shell:
  "Rscript {input.script}"
  " -i {input.consensus}"

diff --git a/analyses/copy_number_consensus_call_manta/results/cnv-consensus-freec-ckit-manta.seg.gz b/analyses/copy_number_consensus_call_manta/results/cnv-consensus-freec-ckit-manta.seg.gz
diff --git a/analyses/copy_number_consensus_call_manta/results/cnv-consensus.seg.gz b/analyses/copy_number_consensus_call_manta/results/cnv-consensus.seg.gz