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* Telephone number for medical questions in the report (#32) * updated version in configs * Removed print statements * Added telephone number in the report for medical information * update version in the configs * updated changelog.md * Updated DPYD HAPB3 haplotype related rsids (#33) * Update CHANGELOG.md Signed-off-by: Ram Sai Nanduri <[email protected]> * Added a new module for pharmcat (#35) * reflects v1.1.0 Signed-off-by: Ram Sai Nanduri <[email protected]> * Report update (#37) * Update report text * Updated changelog and added github workflow for changelog reminder * Update README.md Signed-off-by: Ram Sai Nanduri <[email protected]> * Pharmcat update 2.12.0 (#38) * Updated Pharmacat module Updated the sub workflow with respect to pharmcat, now the haplotype filtration takes palce first and then ontarget followed by annotation.. * updated annotation output file name * Updated configs, modules and workflows with respect to pharmcat * Added options for the report - extended report, match all the haplotypes not just the top ones, report title * Updated ReadMe and ChangeLog * Update config (#40) * fixed pharmat memory bug * Updated Changelog * Fixed Zero division error when there is no allele depth for a variant (#43) * Fixed Zero division error when there is no allele depth for a variant * Updated Changelog #42 #43 * Added Fastq support - refactored the structure of the modules , subworkflows and workflows - based on the input the workflows are selected - removed support for HG19 - draft version of the workflow Things to do - add more support for pharmcat - add suport for cnvs --------- Signed-off-by: Ram Sai Nanduri <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| name: "CHANGELOG Reminder" | ||
| on: | ||
| pull_request: | ||
| types: [opened, synchronize, reopened, ready_for_review, labeled, unlabeled] | ||
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| jobs: | ||
| # Enforces the update of a changelog file on every pull request | ||
| changelog: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - uses: dangoslen/changelog-enforcer@v3 | ||
| with: | ||
| changeLogPath: 'CHANGELOG.md' | ||
| skipLabels: 'skip-changelog-update' |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,18 @@ | ||
| #!/usr/bin/perl -w | ||
| use strict; | ||
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| my $in_bed = $ARGV[0]; | ||
| my $genes_bed = $ARGV[1]; | ||
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| my $rnd = int rand 1000000000; | ||
| my $tmp_infile = "input.$rnd.bed"; | ||
| system("grep -v '^\@' $in_bed| grep -v ^CONTIG| grep -v ^REF > $tmp_infile"); | ||
| my @overlap = `bedtools intersect -a $tmp_infile -b $genes_bed -loj`; | ||
| unlink $tmp_infile; | ||
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| foreach my $line (@overlap) { | ||
| chomp $line; | ||
| my @f = split /\t/, $line; | ||
| print "$f[0]\t$f[1]\t$f[2]\t$f[3]\t$f[-1]\n"; | ||
| } | ||
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| @@ -0,0 +1,47 @@ | ||
| #!/usr/bin/perl -w | ||
| use strict; | ||
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| my $cutoff = 500; | ||
| die "USAGE: panel_depth.pl BAM BED\n" unless @ARGV == 2; | ||
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| my( $bam, $bed ) = ( $ARGV[0], $ARGV[1] ); | ||
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| die "No file $bam" unless -s $bam; | ||
| die "No file $bed" unless -s $bed; | ||
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| open( DEPTH, "sambamba depth base $bam -L $bed |" ); | ||
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| my( $start_pos, $start_chr, $last_low_pos, $last_low_chr, $low_cov_sum ); | ||
| while( <DEPTH> ) { | ||
| my @a = split /\t/; | ||
| my( $chr, $pos, $depth ) = ( $a[0], $a[1], $a[2] ); | ||
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| if( $depth < $cutoff ) { | ||
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| # Prev low position was right before | ||
| if( $last_low_chr and $last_low_pos and $last_low_chr eq $chr and $last_low_pos == $pos-1 ) { | ||
| # Skip along low depth region | ||
| $low_cov_sum += $depth; | ||
| } | ||
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| # Prev low postion was somewhere else | ||
| else { | ||
| if( $start_pos and $start_chr ) { | ||
| print $start_chr."\t".$start_pos."\t".$last_low_pos."\t".($low_cov_sum/($last_low_pos-$start_pos+1))."\n"; | ||
| } | ||
| $start_chr = $chr; | ||
| $start_pos = $pos; | ||
| $low_cov_sum = $depth; | ||
| } | ||
| $last_low_chr = $chr; | ||
| $last_low_pos = $pos; | ||
| } | ||
| else { | ||
| if( $start_chr and $start_pos ) { | ||
| print $start_chr."\t".$start_pos."\t".$last_low_pos."\t".($low_cov_sum/($last_low_pos-$start_pos+1))."\n"; | ||
| undef $start_chr; | ||
| undef $start_pos; | ||
| } | ||
| } | ||
| } |
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