From 7c79779594fa77c8f5fbbee70b4ddb4888ea5553 Mon Sep 17 00:00:00 2001 From: aknecht2 <aknecht2@unl.edu> Date: Sat, 9 Apr 2016 16:06:02 -0500 Subject: [PATCH] Updated conf to include tagalign files. Renamed script files from wrappers. Added cat_spp for ungzipped results. Updated peak_call.yaml to rename .bed files to .tagAlign for spp. --- chipathlon/conf.py | 2 +- chipathlon/jobs/modules/peak_call.yaml | 20 ++++++++++++++++-- .../jobs/params/cat_awk_sort_peaks.yaml | 21 +++++++++++++++++++ chipathlon/jobs/params/mv_bed_tagalign.yaml | 21 +++++++++++++++++++ .../jobs/params/sort_awk_sort_peaks.yaml | 2 +- .../jobs/params/zcat_awk_sort_peaks.yaml | 2 +- chipathlon/jobs/scripts/cat_spp.sh | 3 +++ chipathlon/jobs/scripts/mv_bed_tagalign.sh | 3 +++ .../{sort_wrapper.sh => sort_macs2.sh} | 0 .../scripts/{zcat_wrapper.sh => zcat_spp.sh} | 0 10 files changed, 69 insertions(+), 5 deletions(-) create mode 100644 chipathlon/jobs/params/cat_awk_sort_peaks.yaml create mode 100644 chipathlon/jobs/params/mv_bed_tagalign.yaml create mode 100644 chipathlon/jobs/scripts/cat_spp.sh create mode 100644 chipathlon/jobs/scripts/mv_bed_tagalign.sh rename chipathlon/jobs/scripts/{sort_wrapper.sh => sort_macs2.sh} (100%) rename chipathlon/jobs/scripts/{zcat_wrapper.sh => zcat_spp.sh} (100%) diff --git a/chipathlon/conf.py b/chipathlon/conf.py index 38c2691..b76e140 100644 --- a/chipathlon/conf.py +++ b/chipathlon/conf.py @@ -17,7 +17,7 @@ file_extensions = { "sai": ["sai"], "sam": ["sam"], "bam": ["bam"], - "bed": ["bed", "narrowPeak", "broadPeak"], + "bed": ["bed", "narrowPeak", "broadPeak", "tagAlign"], "bwa_genome": ["amb", "ann", "bwt", "pac", "sa"], "bowtie2_genome": ["1.bt2", "2.bt2", "3.bt2", "4.bt2", "rev.1.bt2", "rev.2.bt2"], "quality": ["quality"], diff --git a/chipathlon/jobs/modules/peak_call.yaml b/chipathlon/jobs/modules/peak_call.yaml index 3f68d0a..ea10a30 100644 --- a/chipathlon/jobs/modules/peak_call.yaml +++ b/chipathlon/jobs/modules/peak_call.yaml @@ -1,12 +1,28 @@ peak_call: - spp[tool]: - - r_spp_nodups: + - mv_bed_tagalign: inputs: - exp.bed: type: file + additional_inputs: null + outputs: + - exp.tagAlign: + type: file + - mv_bed_tagalign: + inputs: - control.bed: type: file additional_inputs: null + outputs: + - control.tagAlign: + type: file + - r_spp_nodups: + inputs: + - exp.tagAlign: + type: file + - control.tagAlign: + type: file + additional_inputs: null outputs: - results.narrowPeak: type: file @@ -14,7 +30,7 @@ peak_call: type: file - results.ccscore: type: file - - zcat_awk_sort_peaks: + - cat_awk_sort_peaks: inputs: - results.narrowPeak: type: file diff --git a/chipathlon/jobs/params/cat_awk_sort_peaks.yaml b/chipathlon/jobs/params/cat_awk_sort_peaks.yaml new file mode 100644 index 0000000..d4cafc0 --- /dev/null +++ b/chipathlon/jobs/params/cat_awk_sort_peaks.yaml @@ -0,0 +1,21 @@ +cat_awk_sort_peaks: + inputs: + - bed: + type: file + additional_inputs: null + outputs: + - bed: + type: file + command: cat_spp + arguments: + - "$inputs.0": + changeable: false + required: true + has_value: false + - "$outputs.0": + changeable: false + required: true + has_value: false + walltime: 2000 + memory: 2000 + cores: 1 diff --git a/chipathlon/jobs/params/mv_bed_tagalign.yaml b/chipathlon/jobs/params/mv_bed_tagalign.yaml new file mode 100644 index 0000000..5b54086 --- /dev/null +++ b/chipathlon/jobs/params/mv_bed_tagalign.yaml @@ -0,0 +1,21 @@ +zcat_awk_sort_peaks: + inputs: + - bed: + type: file + additional_inputs: null + outputs: + - bed: + type: file + command: mv_bed_tagalign + arguments: + - "$inputs.0": + changeable: false + required: true + has_value: false + - "$outputs.0": + changeable: false + required: true + has_value: false + walltime: 2000 + memory: 2000 + cores: 1 diff --git a/chipathlon/jobs/params/sort_awk_sort_peaks.yaml b/chipathlon/jobs/params/sort_awk_sort_peaks.yaml index 1271f40..3979e68 100644 --- a/chipathlon/jobs/params/sort_awk_sort_peaks.yaml +++ b/chipathlon/jobs/params/sort_awk_sort_peaks.yaml @@ -6,7 +6,7 @@ sort_awk_sort_peaks: outputs: - bed: type: file - command: sort + command: sort_macs2 arguments: - "$inputs.0": changeable: false diff --git a/chipathlon/jobs/params/zcat_awk_sort_peaks.yaml b/chipathlon/jobs/params/zcat_awk_sort_peaks.yaml index f226897..cebf20e 100644 --- a/chipathlon/jobs/params/zcat_awk_sort_peaks.yaml +++ b/chipathlon/jobs/params/zcat_awk_sort_peaks.yaml @@ -6,7 +6,7 @@ zcat_awk_sort_peaks: outputs: - bed: type: file - command: zcat + command: zcat_spp arguments: - "$inputs.0": changeable: false diff --git a/chipathlon/jobs/scripts/cat_spp.sh b/chipathlon/jobs/scripts/cat_spp.sh new file mode 100644 index 0000000..54abba4 --- /dev/null +++ b/chipathlon/jobs/scripts/cat_spp.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +/bin/cat "$1" | awk 'BEGIN{OFS="\t"}{print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' > "$2" diff --git a/chipathlon/jobs/scripts/mv_bed_tagalign.sh b/chipathlon/jobs/scripts/mv_bed_tagalign.sh new file mode 100644 index 0000000..f5def69 --- /dev/null +++ b/chipathlon/jobs/scripts/mv_bed_tagalign.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +/bin/mv "$1" "$2" diff --git a/chipathlon/jobs/scripts/sort_wrapper.sh b/chipathlon/jobs/scripts/sort_macs2.sh similarity index 100% rename from chipathlon/jobs/scripts/sort_wrapper.sh rename to chipathlon/jobs/scripts/sort_macs2.sh diff --git a/chipathlon/jobs/scripts/zcat_wrapper.sh b/chipathlon/jobs/scripts/zcat_spp.sh similarity index 100% rename from chipathlon/jobs/scripts/zcat_wrapper.sh rename to chipathlon/jobs/scripts/zcat_spp.sh -- GitLab