Refactor and cleanup

hartwigmedical · May 29, 2018 · 0c3ce1d · 0c3ce1d
1 parent e1b3b91
commit 0c3ce1d
Show file tree

Hide file tree

Showing 10 changed files with 14 additions and 15 deletions.
diff --git a/lib/HMF/Pipeline/Functions/Bam.pm b/lib/HMF/Pipeline/Functions/Bam.pm
@@ -29,7 +29,7 @@ sub sorted {
 
     my $sorted_bam_name = fileparse($sorted_bam_path);
     return fromTemplate(
-        "SortBam",
+        "BamSort",
         $sorted_bam_name,
         0,
         qsubTemplate($opt, "MAPPING"),
@@ -48,7 +48,7 @@ sub slice {
 
     my $slice_name = fileparse($sliced_bam);
     return fromTemplate(
-        "SliceBam",
+        "BamSlice",
         $slice_name,
         0,
         qsubTemplate($opt, "FLAGSTAT"),
@@ -69,7 +69,7 @@ sub indexed {
 
     my $bai_name = fileparse($bai_path);
     return fromTemplate(
-        "IndexBam",
+        "BamIndex",
         $bai_name,
         0,
         qsubTemplate($opt, "MAPPING"),
@@ -87,7 +87,7 @@ sub flagstat {
 
     my $flagstat_name = fileparse($flagstat_path);
     return fromTemplate(
-        "Flagstat",
+        "BamFlagstat",
         $flagstat_name,
         0,
         qsubTemplate($opt, "FLAGSTAT"),
@@ -106,7 +106,7 @@ sub readCountCheck {
 
     my $post_flagstat_name = fileparse($post_flagstat_path);
     return fromTemplate(
-        "ReadCountCheck",
+        "BamReadCountCheck",
         $post_flagstat_name,
         0,
         qsubTemplate($opt, "FLAGSTAT"),
@@ -126,7 +126,7 @@ sub diff {
     my ($step, $input_bam1, $input_bam2, $diff_name, $hold_jids, $dirs, $opt) = @_;
 
     return fromTemplate(
-        "DiffBams",
+        "BamDiff",
         $diff_name,
         0,
         qsubTemplate($opt, "FLAGSTAT"),

diff --git a/lib/HMF/Pipeline/Mapping.pm b/lib/HMF/Pipeline/Mapping.pm
@@ -172,7 +172,7 @@ sub runBamPrepOnSample {
         my $index_job_id = indexed($sample, $sample_bam, $sample_bai, [], $dirs, $opt);
         my $flagstat_job_id = flagstat($sample, $sample_bam, $sample_flagstat, [$index_job_id], $dirs, $opt);
         my $check_job_id = fromTemplate(
-            "ContigCheck",
+            "BamContigCheck",
             $sample,
             0,
             qsubSimple($opt),

diff --git a/requirements.txt b/requirements.txt
@@ -1,2 +1 @@
 Cython==0.25.2
-PyVCF==0.6.8
diff --git a/templates/ContigCheck.sh.tt → templates/BamContigCheck.sh.tt b/templates/ContigCheck.sh.tt → templates/BamContigCheck.sh.tt
@@ -2,7 +2,7 @@
 # -*- TT -*-
 
 [% INCLUDE ErrorHandling.tt %]
-[% INCLUDE Logging.tt job_name="ContigCheck" main_step=bam_path log_name="${step}.log" %]
+[% INCLUDE Logging.tt job_name="BamContigCheck" main_step=bam_path log_name="${step}.log" %]
 
 assert_not_empty "[% bam_path %]" "[% bam_path %].bai"
 

diff --git a/templates/DiffBams.sh.tt → templates/BamDiff.sh.tt b/templates/DiffBams.sh.tt → templates/BamDiff.sh.tt
@@ -2,7 +2,7 @@
 # -*- TT -*-
 
 [% INCLUDE ErrorHandling.tt %]
-[% INCLUDE Logging.tt job_name="DiffBams" main_step=diff_name log_name="${step}.log" %]
+[% INCLUDE Logging.tt job_name="BamDiff" main_step=diff_name log_name="${step}.log" %]
 
 assert_not_empty "[% input_bam1 %]" "[% input_bam2 %]"
 

diff --git a/templates/Flagstat.sh.tt → templates/BamFlagstat.sh.tt b/templates/Flagstat.sh.tt → templates/BamFlagstat.sh.tt
@@ -2,7 +2,7 @@
 # -*- TT -*-
 
 [% INCLUDE ErrorHandling.tt %]
-[% INCLUDE Logging.tt job_name="Flagstat" main_step=flagstat_name log_name="${step}.log" %]
+[% INCLUDE Logging.tt job_name="BamFlagstat" main_step=flagstat_name log_name="${step}.log" %]
 
 assert_not_empty "[% bam_path %]"
 

diff --git a/templates/IndexBam.sh.tt → templates/BamIndex.sh.tt b/templates/IndexBam.sh.tt → templates/BamIndex.sh.tt
@@ -2,7 +2,7 @@
 # -*- TT -*-
 
 [% INCLUDE ErrorHandling.tt %]
-[% INCLUDE Logging.tt job_name="IndexBam" main_step=bam_path log_name="${step}.log" %]
+[% INCLUDE Logging.tt job_name="BamIndex" main_step=bam_path log_name="${step}.log" %]
 
 assert_not_empty "[% bam_path %]"
 

diff --git a/templates/ReadCountCheck.sh.tt → templates/BamReadCountCheck.sh.tt b/templates/ReadCountCheck.sh.tt → templates/BamReadCountCheck.sh.tt
@@ -2,7 +2,7 @@
 # -*- TT -*-
 
 [% INCLUDE ErrorHandling.tt %]
-[% INCLUDE Logging.tt job_name="ReadCountCheck" main_step=post_flagstat_name log_name="${step}.log" %]
+[% INCLUDE Logging.tt job_name="BamReadCountCheck" main_step=post_flagstat_name log_name="${step}.log" %]
 
 assert_not_empty "[% pre_flagstat_paths.join('" "') %]" "[% post_flagstat_path %]"
 

diff --git a/templates/SliceBam.sh.tt → templates/BamSlice.sh.tt b/templates/SliceBam.sh.tt → templates/BamSlice.sh.tt
@@ -2,7 +2,7 @@
 # -*- TT -*-
 
 [% INCLUDE ErrorHandling.tt %]
-[% INCLUDE Logging.tt job_name="SliceBam" main_step=slice_name log_name="${step}.log" %]
+[% INCLUDE Logging.tt job_name="BamSlice" main_step=slice_name log_name="${step}.log" %]
 
 assert_not_empty "[% input_bam %]"
 

diff --git a/templates/SortBam.sh.tt → templates/BamSort.sh.tt b/templates/SortBam.sh.tt → templates/BamSort.sh.tt
@@ -2,7 +2,7 @@
 # -*- TT -*-
 
 [% INCLUDE ErrorHandling.tt %]
-[% INCLUDE Logging.tt job_name="SortBam" main_step=sorted_bam_name log_name="${step}.log" %]
+[% INCLUDE Logging.tt job_name="BamSort" main_step=sorted_bam_name log_name="${step}.log" %]
 
 assert_not_empty "[% bam_path %]"