Mercurial > repos > stef > falco
changeset 75:3515b026d78b draft
Uploaded
| author | stef |
|---|---|
| date | Fri, 27 Feb 2015 09:57:21 -0500 |
| parents | 00f63511d177 |
| children | 379604c84f5b |
| files | falco-filter-report.sh falco-filter-report.xml falco/bin/falco-filter-report falco/lib/perl/filter.pl |
| diffstat | 4 files changed, 15 insertions(+), 24 deletions(-) [+] |
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--- a/falco-filter-report.sh Fri Feb 27 09:45:42 2015 -0500 +++ b/falco-filter-report.sh Fri Feb 27 09:57:21 2015 -0500 @@ -20,13 +20,6 @@ ## ---------- ## set params ## ---------- -if [[ $canonicals_file != 'None' && $canonicals_file != '' ]] # Galaxy default is "None" for some reason -then - CANONICALS_PARAM=" --canonicals "$canonicals_file -else - CANONICALS_PARAM="" -fi - if [[ $vcf2_file != 'None' && $vcf2_file != '' ]] # Galaxy default is "None" for some reason then VCF2_PARAM=" --vcfOther "$vcf2_file @@ -73,7 +66,7 @@ ## running analysis ## ---------- echo "[INFO] Starting FALCO reporting" -CMD_STRING="$TOOLDIR/falco/bin/falco-filter-report --vcf $vcf_file --output $vcf_base --qc_ann_qual_txt $qc_ann_qual_file --qc2_ann_txt $qc2_ann_txt_file --qc_targets_txt $qc_targets_txt_file $VCF2_PARAM $CANONICALS_PARAM" +CMD_STRING="$TOOLDIR/falco/bin/falco-filter-report --vcf $vcf_file --output $vcf_base --qc_ann_qual_txt $qc_ann_qual_file --qc2_ann_txt $qc2_ann_txt_file --qc_targets_txt $qc_targets_txt_file $VCF2_PARAM" echo "[INFO] "$CMD_STRING perl $CMD_STRING echo "[INFO] done with FALCO reporting"
--- a/falco-filter-report.xml Fri Feb 27 09:45:42 2015 -0500 +++ b/falco-filter-report.xml Fri Feb 27 09:57:21 2015 -0500 @@ -44,13 +44,12 @@ <validator type="empty_field" /> <validator type="regex" message="This field may contain only non-whitespace characters">\S+</validator> </param> - <param name="vcf" type="data" multiple="false" optional="false" format="vcf" label="Input VCF" help="Select snpeff annotated VCF file" /> - <param name="vcf2" type="data" multiple="false" optional="true" format="vcf" label="Input VCF (optional second)" help="FALCO pipeline is often run with samtools as second caller" /> + <param name="vcf" type="data" multiple="false" optional="false" format="vcf" label="Input VCF" help="NOTE: VCF must be annotated with SNPEFF (should contain \"EFF\" FIELD)" /> + <param name="vcf2" type="data" multiple="false" optional="true" format="vcf" label="Input VCF (optional second VCF)" help="NOTE: VCF must be annotated with SNPEFF (should contain \"EFF\" FIELD)" /> - <param format="tsv" name="qc_ann_qual" optional="false" type="data" label="qc_ann_qual file" help=""/> - <param format="tsv" name="qc2_ann_txt" optional="false" type="data" label="qc2_ann_txt file" help=""/> - <param format="tsv" name="qc_targets_txt" optional="false" type="data" label="qc_targets_txt file" help=""/> - <param format="tsv" name="canonicals" optional="true" type="data" label="canonicals file" help=""/> + <param format="tsv" name="qc_ann_qual" optional="false" type="data" label="qc_ann_qual file" help="This file is output of the FALCO variant caller"/> + <param format="tsv" name="qc2_ann_txt" optional="false" type="data" label="qc2_ann_txt file" help="This file is output of the FALCO variant caller"/> + <param format="tsv" name="qc_targets_txt" optional="false" type="data" label="qc_targets_txt file" help="This file is output of the FALCO variant caller"/> <!-- ==================== --> <!-- Option to use your own bin annotations -->
--- a/falco/bin/falco-filter-report Fri Feb 27 09:45:42 2015 -0500 +++ b/falco/bin/falco-filter-report Fri Feb 27 09:57:21 2015 -0500 @@ -36,7 +36,6 @@ "vcf=s" => \$vcf, "vcfOther=s" => \$vcfOther, "output=s" => \$base, - "canonicals=s" => \$canonicals, "clinvar=s" => \$clinvar, "cosmic=s" => \$cosmic, "cosmicNC=s" => \$cosmicNC,
--- a/falco/lib/perl/filter.pl Fri Feb 27 09:45:42 2015 -0500 +++ b/falco/lib/perl/filter.pl Fri Feb 27 09:57:21 2015 -0500 @@ -81,15 +81,15 @@ $trans =~ s/\..*$//; ## impossible to switch off these two transcript filters - ## so comment these out if no other way provided - if (not exists($nm{$trans})) { - print STDERR "Unknown transcript: $row[$col{Gene_Name}] $trans\n"; - next; - } - elsif ($nm{$trans} != 0) { - print STDERR "Non cannonical: $row[$col{Gene_Name}] $trans\n"; - next; - } + ## so commented out + # if (not exists($nm{$trans})) { + # print STDERR "Unknown transcript: $row[$col{Gene_Name}] $trans\n"; + # next; + # } + # elsif ($nm{$trans} != 0) { + # print STDERR "Non cannonical: $row[$col{Gene_Name}] $trans\n"; + # next; + # } # Annotate clinincal variants and cosmic mutations