Changed comments in classes' default config.

bihealth · Jun 22, 2021 · 9e64d82 · 9e64d82
1 parent 31200eb
commit 9e64d82
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Showing 8 changed files with 40 additions and 20 deletions.
diff --git a/snappy_pipeline/workflows/panel_of_normals/__init__.py b/snappy_pipeline/workflows/panel_of_normals/__init__.py
@@ -102,7 +102,8 @@
       job_mult_time: 1           # running time multiplier
       merge_mult_memory: 1       # memory multiplier for merging
       merge_mult_time: 1         # running time multiplier for merging
-      ignore_chroms:             # patterns of chromosome names to ignore
+      # patterns of chromosome names to ignore
+      ignore_chroms:
       - NC_007605    # herpes virus
       - hs37d5       # GRCh37 decoy
       - chrEBV       # Eppstein-Barr Virus

diff --git a/snappy_pipeline/workflows/somatic_variant_annotation/__init__.py b/snappy_pipeline/workflows/somatic_variant_annotation/__init__.py
@@ -85,7 +85,8 @@
     restart_times: 5          # number of times to re-launch jobs in case of failure
     max_jobs_per_second: 10   # throttling of job creation
     max_status_checks_per_second: 10   # throttling of status checks
-    ignore_chroms:            # patterns of chromosome names to ignore
+    # patterns of chromosome names to ignore
+    ignore_chroms:
     - NC_007605  # herpes virus
     - hs37d5     # GRCh37 decoy
     - chrEBV     # Eppstein-Barr Virus

diff --git a/snappy_pipeline/workflows/somatic_variant_calling/__init__.py b/snappy_pipeline/workflows/somatic_variant_calling/__init__.py
@@ -187,7 +187,8 @@
       max_indel_depth: 4000
       window_length: 10000000
       num_threads: 16
-      ignore_chroms:            # patterns of chromosome names to ignore
+      # patterns of chromosome names to ignore
+      ignore_chroms:
       - NC_007605    # herpes virus
       - hs37d5       # GRCh37 decoy
       - chrEBV       # Eppstein-Barr Virus
@@ -198,7 +199,8 @@
     platypus_joint:
       split_complex_mnvs: true  # whether or not to split complex and MNV variants
       num_threads: 16
-      ignore_chroms:            # patterns of chromosome names to ignore
+      # patterns of chromosome names to ignore
+      ignore_chroms:
       - NC_007605    # herpes virus
       - hs37d5       # GRCh37 decoy
       - chrEBV       # Eppstein-Barr Virus
@@ -226,7 +228,8 @@
       job_mult_time: 1           # running time multiplier
       merge_mult_memory: 1       # memory multiplier for merging
       merge_mult_time: 1         # running time multiplier for merging
-      ignore_chroms:             # patterns of chromosome names to ignore
+      # patterns of chromosome names to ignore
+      ignore_chroms:
       - NC_007605    # herpes virus
       - hs37d5       # GRCh37 decoy
       - chrEBV       # Eppstein-Barr Virus
@@ -253,7 +256,8 @@
       job_mult_time: 1          # running time multiplier
       merge_mult_memory: 1      # memory multiplier for merging
       merge_mult_time: 1        # running time multiplier for merging
-      ignore_chroms:            # patterns of chromosome names to ignore
+      # patterns of chromosome names to ignore
+      ignore_chroms:
       - NC_007605    # herpes virus
       - hs37d5       # GRCh37 decoy
       - chrEBV       # Eppstein-Barr Virus
@@ -282,7 +286,8 @@
       job_mult_time: 1          # running time multiplier
       merge_mult_memory: 1      # memory multiplier for merging
       merge_mult_time: 1        # running time multiplier for merging
-      ignore_chroms:            # patterns of chromosome names to ignore
+      # patterns of chromosome names to ignore
+      ignore_chroms:
       - NC_007605    # herpes virus
       - hs37d5       # GRCh37 decoy
       - chrEBV       # Eppstein-Barr Virus
@@ -322,7 +327,8 @@
       job_mult_time: 1          # running time multiplier
       merge_mult_memory: 1      # memory multiplier for merging
       merge_mult_time: 1        # running time multiplier for merging
-      ignore_chroms:            # patterns of chromosome names to ignore
+      # patterns of chromosome names to ignore
+      ignore_chroms:
       - NC_007605    # herpes virus
       - hs37d5       # GRCh37 decoy
       - chrEBV       # Eppstein-Barr Virus
@@ -357,7 +363,8 @@
       restart_times: 5          # number of times to re-launch jobs in case of failure
       max_jobs_per_second: 2    # throttling of job creation
       max_status_checks_per_second: 10   # throttling of status checks
-      ignore_chroms:            # patterns of chromosome names to ignore
+      # patterns of chromosome names to ignore
+      ignore_chroms:
       - NC_007605    # herpes virus
       - hs37d5       # GRCh37 decoy
       - chrEBV       # Eppstein-Barr Virus

diff --git a/snappy_pipeline/workflows/somatic_variant_filtration/__init__.py b/snappy_pipeline/workflows/somatic_variant_filtration/__init__.py
@@ -116,7 +116,8 @@
       job_mult_time: 1          # running time multiplier
       merge_mult_memory: 1      # memory multiplier for merging
       merge_mult_time: 1        # running time multiplier for merging
-      ignore_chroms:            # patterns of chromosome names to ignore
+      # patterns of chromosome names to ignore
+      ignore_chroms:
       - NC_007605    # herpes virus
       - hs37d5       # GRCh37 decoy
       - chrEBV       # Eppstein-Barr Virus

diff --git a/snappy_pipeline/workflows/variant_annotation/__init__.py b/snappy_pipeline/workflows/variant_annotation/__init__.py
@@ -214,7 +214,8 @@
     job_mult_time: 1          # running time multiplier
     merge_mult_memory: 1      # memory multiplier for merging
     merge_mult_time: 1        # running time multiplier for merging
-    ignore_chroms:            # patterns of chromosome names to ignore
+    # patterns of chromosome names to ignore
+    ignore_chroms:
     - NC_007605  # herpes virus
     - hs37d5     # GRCh37 decoy
     - chrEBV     # Eppstein-Barr Virus

diff --git a/snappy_pipeline/workflows/variant_calling/__init__.py b/snappy_pipeline/workflows/variant_calling/__init__.py
@@ -188,7 +188,8 @@
       path_ser: REQUIRED  # REQUIRED
     platypus:
       num_threads: 16
-      ignore_chroms:            # patterns of chromosome names to ignore
+      # patterns of chromosome names to ignore
+      ignore_chroms:
       - NC_007605  # herpes virus
       - hs37d5     # GRCh37 decoy
       - chrEBV     # Eppstein-Barr Virus
@@ -199,7 +200,8 @@
       max_indel_depth: 4000
       window_length: 10000000
       num_threads: 16
-      ignore_chroms:            # patterns of chromosome names to ignore
+      # patterns of chromosome names to ignore
+      ignore_chroms:
       - NC_007605  # herpes virus
       - hs37d5     # GRCh37 decoy
       - chrEBV     # Eppstein-Barr Virus
@@ -209,7 +211,8 @@
       use_standard_filters: true
       window_length: 10000000
       num_threads: 16
-      ignore_chroms:            # patterns of chromosome names to ignore
+      # patterns of chromosome names to ignore
+      ignore_chroms:
       - NC_007605  # herpes virus
       - hs37d5     # GRCh37 decoy
       - chrEBV     # Eppstein-Barr Virus
@@ -231,7 +234,8 @@
       job_mult_time: 1          # running time multiplier
       merge_mult_memory: 1      # memory multiplier for merging
       merge_mult_time: 1        # running time multiplier for merging
-      ignore_chroms:            # patterns of chromosome names to ignore
+      # patterns of chromosome names to ignore
+      ignore_chroms:
       - NC_007605  # herpes virus
       - hs37d5     # GRCh37 decoy
       - chrEBV     # Eppstein-Barr Virus
@@ -270,7 +274,8 @@
       restart_times: 10         # number of times to re-launch jobs in case of failure
       max_jobs_per_second: 10   # throttling of job creation
       max_status_checks_per_second: 10  # throttling of status jobs
-      ignore_chroms:            # patterns of chromosome names to ignore
+      # patterns of chromosome names to ignore
+      ignore_chroms:
       - NC_007605  # herpes virus
       - hs37d5     # GRCh37 decoy
       - chrEBV     # Eppstein-Barr Virus
@@ -309,7 +314,8 @@
       job_mult_time: 1          # running time multiplier
       merge_mult_memory: 1      # memory multiplier for merging
       merge_mult_time: 1        # running time multiplier for merging
-      ignore_chroms:            # patterns of chromosome names to ignore
+      # patterns of chromosome names to ignore
+      ignore_chroms:
       - NC_007605  # herpes virus
       - hs37d5     # GRCh37 decoy
       - chrEBV     # Eppstein-Barr Virus
@@ -358,7 +364,8 @@
       job_mult_time: 1          # running time multiplier
       merge_mult_memory: 1      # memory multiplier for merging
       merge_mult_time: 1        # running time multiplier for merging
-      ignore_chroms:            # patterns of chromosome names to ignore
+      # patterns of chromosome names to ignore
+      ignore_chroms:
       - nc_007605  # herpes virus
       - hs37d5     # grch37 decoy
       - chrebv     # eppstein-barr virus

diff --git a/snappy_pipeline/workflows/variant_denovo_filtration/__init__.py b/snappy_pipeline/workflows/variant_denovo_filtration/__init__.py
@@ -127,7 +127,8 @@
     tools_variant_calling: null      # defaults to variant_annotation tool
     info_key_reliable_regions: []    # optional INFO keys with reliable regions
     info_key_unreliable_regions: []  # optional INFO keys with unreliable regions
-    params_besenbacher:              # parameters for Besenbacher quality filter
+    # parameters for Besenbacher quality filter
+    params_besenbacher:
       min_gq: 50
       min_dp: 10
       max_dp: 120

diff --git a/snappy_pipeline/workflows/variant_phasing/__init__.py b/snappy_pipeline/workflows/variant_phasing/__init__.py
@@ -111,7 +111,8 @@
       job_mult_time: 1          # running time multiplier
       merge_mult_memory: 1      # memory multiplier for merging
       merge_mult_time: 1        # running time multiplier for merging
-      ignore_chroms:            # patterns of chromosome names to ignore
+      # patterns of chromosome names to ignore
+      ignore_chroms:
       - NC_007605               # herpes virus
       - hs37d5                  # GRCh37 decoy
       - chrEBV                  # Eppstein-Barr Virus