From 304e0890af69273eeb20835f3b0de1f3c421bf8c Mon Sep 17 00:00:00 2001 From: aknecht2 <aknecht2@unl.edu> Date: Thu, 4 May 2017 12:40:28 -0500 Subject: [PATCH] A start... --- chipathlon/jobs/params/bedtools_bam_to_bed.yaml | 2 +- chipathlon/jobs/params/bowtie2_align_paired.yaml | 4 ++-- chipathlon/jobs/params/bowtie2_align_single.yaml | 4 ++-- chipathlon/jobs/params/bwa_align_paired.yaml | 2 +- chipathlon/jobs/params/bwa_align_single.yaml | 2 +- chipathlon/jobs/params/cat_awk_sort_peaks.yaml | 2 +- chipathlon/jobs/params/ccat_callpeak.yaml | 2 +- chipathlon/jobs/params/chr_locus_convert.yaml | 2 +- chipathlon/jobs/params/cp.yaml | 2 +- chipathlon/jobs/params/db_save_result.yaml | 4 ++-- chipathlon/jobs/params/download_from_encode.yaml | 2 +- chipathlon/jobs/params/download_from_gridfs.yaml | 2 +- chipathlon/jobs/params/gem_callpeak.yaml | 2 +- chipathlon/jobs/params/idr.yaml | 4 ++-- chipathlon/jobs/params/macs2_broad.yaml | 4 ++-- chipathlon/jobs/params/macs2_narrow.yaml | 4 ++-- chipathlon/jobs/params/music_broad.yaml | 2 +- chipathlon/jobs/params/music_narrow.yaml | 2 +- chipathlon/jobs/params/music_punctate.yaml | 2 +- chipathlon/jobs/params/peakranger_callpeak.yaml | 4 ++-- chipathlon/jobs/params/peakranger_format_bed.yaml | 2 +- chipathlon/jobs/params/picard_clean_sam.yaml | 2 +- chipathlon/jobs/params/picard_mark_duplicates.yaml | 2 +- chipathlon/jobs/params/picard_sort_sam.yaml | 2 +- chipathlon/jobs/params/samtools_filter_bam.yaml | 2 +- chipathlon/jobs/params/samtools_remove_duplicates.yaml | 2 +- chipathlon/jobs/params/samtools_sam_to_bam.yaml | 2 +- chipathlon/jobs/params/sort_awk_sort_peaks.yaml | 2 +- chipathlon/jobs/params/spp_nodups_broad.yaml | 2 +- chipathlon/jobs/params/spp_nodups_narrow.yaml | 2 +- chipathlon/jobs/params/zcat_awk_sort_peaks.yaml | 2 +- 31 files changed, 38 insertions(+), 38 deletions(-) diff --git a/chipathlon/jobs/params/bedtools_bam_to_bed.yaml b/chipathlon/jobs/params/bedtools_bam_to_bed.yaml index 32c67a0..a0eaf3e 100644 --- a/chipathlon/jobs/params/bedtools_bam_to_bed.yaml +++ b/chipathlon/jobs/params/bedtools_bam_to_bed.yaml @@ -21,7 +21,7 @@ bedtools_bam_to_bed: required: true has_value: true default: $inputs.0 - walltime: 2000 + walltime: 60 memory: 2000 cores: 1 nodes: 1 diff --git a/chipathlon/jobs/params/bowtie2_align_paired.yaml b/chipathlon/jobs/params/bowtie2_align_paired.yaml index 342f129..432fa58 100644 --- a/chipathlon/jobs/params/bowtie2_align_paired.yaml +++ b/chipathlon/jobs/params/bowtie2_align_paired.yaml @@ -78,7 +78,7 @@ bowtie2_align_paired: required: false has_value: true default: 8 - walltime: 2000 - memory: 2000 + walltime: 1440 + memory: 8000 cores: 8 nodes: 1 diff --git a/chipathlon/jobs/params/bowtie2_align_single.yaml b/chipathlon/jobs/params/bowtie2_align_single.yaml index 7e30a3e..e40ef86 100644 --- a/chipathlon/jobs/params/bowtie2_align_single.yaml +++ b/chipathlon/jobs/params/bowtie2_align_single.yaml @@ -68,7 +68,7 @@ bowtie2_align_single: required: false has_value: true default: 8 - walltime: 2000 - memory: 2000 + walltime: 1440 + memory: 8000 cores: 8 nodes: 1 diff --git a/chipathlon/jobs/params/bwa_align_paired.yaml b/chipathlon/jobs/params/bwa_align_paired.yaml index 2e479e6..d76a020 100644 --- a/chipathlon/jobs/params/bwa_align_paired.yaml +++ b/chipathlon/jobs/params/bwa_align_paired.yaml @@ -68,7 +68,7 @@ bwa_align_paired: changeable: false required: true has_value: false - walltime: 960 + walltime: 1440 memory: 16000 cores: 8 nodes: 1 diff --git a/chipathlon/jobs/params/bwa_align_single.yaml b/chipathlon/jobs/params/bwa_align_single.yaml index ddbe95d..02c03a3 100644 --- a/chipathlon/jobs/params/bwa_align_single.yaml +++ b/chipathlon/jobs/params/bwa_align_single.yaml @@ -78,7 +78,7 @@ bwa_align_single: changeable: false required: true has_value: false - walltime: 960 + walltime: 1440 memory: 16000 cores: 8 nodes: 1 diff --git a/chipathlon/jobs/params/cat_awk_sort_peaks.yaml b/chipathlon/jobs/params/cat_awk_sort_peaks.yaml index 3cdd1f6..5d2f965 100644 --- a/chipathlon/jobs/params/cat_awk_sort_peaks.yaml +++ b/chipathlon/jobs/params/cat_awk_sort_peaks.yaml @@ -20,7 +20,7 @@ cat_awk_sort_peaks: changeable: false required: true has_value: false - walltime: 2000 + walltime: 10 memory: 2000 cores: 1 nodes: 1 diff --git a/chipathlon/jobs/params/ccat_callpeak.yaml b/chipathlon/jobs/params/ccat_callpeak.yaml index 354ed46..8c8a39f 100644 --- a/chipathlon/jobs/params/ccat_callpeak.yaml +++ b/chipathlon/jobs/params/ccat_callpeak.yaml @@ -65,7 +65,7 @@ ccat_callpeak: changeable: false required: true has_value: false - walltime: 120 + walltime: 60 memory: 16000 cores: 1 nodes: 1 diff --git a/chipathlon/jobs/params/chr_locus_convert.yaml b/chipathlon/jobs/params/chr_locus_convert.yaml index 73fa9ce..dc13307 100644 --- a/chipathlon/jobs/params/chr_locus_convert.yaml +++ b/chipathlon/jobs/params/chr_locus_convert.yaml @@ -27,7 +27,7 @@ chr_locus_convert: changeable: false required: true has_value: false - walltime: 120 + walltime: 60 memory: 8000 cores: 1 nodes: 1 diff --git a/chipathlon/jobs/params/cp.yaml b/chipathlon/jobs/params/cp.yaml index f25b6ef..3b50d68 100644 --- a/chipathlon/jobs/params/cp.yaml +++ b/chipathlon/jobs/params/cp.yaml @@ -20,7 +20,7 @@ cp: changeable: false required: true has_value: false - walltime: 2000 + walltime: 10 memory: 2000 cores: 1 nodes: 1 diff --git a/chipathlon/jobs/params/db_save_result.yaml b/chipathlon/jobs/params/db_save_result.yaml index a6d5354..be166a7 100644 --- a/chipathlon/jobs/params/db_save_result.yaml +++ b/chipathlon/jobs/params/db_save_result.yaml @@ -50,7 +50,7 @@ db_save_result: required: true has_value: true default: $inputs.4 - walltime: 2000 - memory: 16000 + walltime: 20 + memory: 2000 cores: 1 nodes: 1 diff --git a/chipathlon/jobs/params/download_from_encode.yaml b/chipathlon/jobs/params/download_from_encode.yaml index 95ff205..be8311a 100644 --- a/chipathlon/jobs/params/download_from_encode.yaml +++ b/chipathlon/jobs/params/download_from_encode.yaml @@ -30,7 +30,7 @@ download_from_encode: required: true has_value: true default: $outputs.0 - walltime: 360 + walltime: 60 memory: 2000 cores: 1 nodes: 1 diff --git a/chipathlon/jobs/params/download_from_gridfs.yaml b/chipathlon/jobs/params/download_from_gridfs.yaml index 3638fa7..1c25a44 100644 --- a/chipathlon/jobs/params/download_from_gridfs.yaml +++ b/chipathlon/jobs/params/download_from_gridfs.yaml @@ -49,6 +49,6 @@ download_from_gridfs: has_value: true default: $outputs.0 walltime: 60 - memory: 8000 + memory: 2000 cores: 1 nodes: 1 diff --git a/chipathlon/jobs/params/gem_callpeak.yaml b/chipathlon/jobs/params/gem_callpeak.yaml index 90973e1..ef52ca8 100644 --- a/chipathlon/jobs/params/gem_callpeak.yaml +++ b/chipathlon/jobs/params/gem_callpeak.yaml @@ -119,7 +119,7 @@ gem_callpeak: required: true has_value: true default: 4 - walltime: 720 + walltime: 780 memory: 16000 cores: 8 nodes: 1 diff --git a/chipathlon/jobs/params/idr.yaml b/chipathlon/jobs/params/idr.yaml index 0d0edcd..cd3be1f 100644 --- a/chipathlon/jobs/params/idr.yaml +++ b/chipathlon/jobs/params/idr.yaml @@ -40,7 +40,7 @@ idr: required: true has_value: true default: $outputs.0 - walltime: 2000 - memory: 16000 + walltime: 600 + memory: 8000 cores: 1 nodes: 1 diff --git a/chipathlon/jobs/params/macs2_broad.yaml b/chipathlon/jobs/params/macs2_broad.yaml index 5f79d9f..e2961b8 100644 --- a/chipathlon/jobs/params/macs2_broad.yaml +++ b/chipathlon/jobs/params/macs2_broad.yaml @@ -99,7 +99,7 @@ macs2_broad: required: true has_value: true default: 0.1 - walltime: 480 - memory: 16000 + walltime: 120 + memory: 8000 cores: 1 nodes: 1 diff --git a/chipathlon/jobs/params/macs2_narrow.yaml b/chipathlon/jobs/params/macs2_narrow.yaml index 175c8e5..9a04a88 100644 --- a/chipathlon/jobs/params/macs2_narrow.yaml +++ b/chipathlon/jobs/params/macs2_narrow.yaml @@ -88,7 +88,7 @@ macs2_narrow: changeable: false required: true has_value: false - walltime: 480 - memory: 16000 + walltime: 120 + memory: 8000 cores: 1 nodes: 1 diff --git a/chipathlon/jobs/params/music_broad.yaml b/chipathlon/jobs/params/music_broad.yaml index de47c09..b30eec6 100644 --- a/chipathlon/jobs/params/music_broad.yaml +++ b/chipathlon/jobs/params/music_broad.yaml @@ -80,6 +80,6 @@ music_broad: has_value: true default: 50 walltime: 240 - memory: 16000 + memory: 8000 cores: 1 nodes: 1 diff --git a/chipathlon/jobs/params/music_narrow.yaml b/chipathlon/jobs/params/music_narrow.yaml index c58c6e5..de7b8cc 100644 --- a/chipathlon/jobs/params/music_narrow.yaml +++ b/chipathlon/jobs/params/music_narrow.yaml @@ -64,6 +64,6 @@ music_narrow: has_value: true default: 50 walltime: 240 - memory: 16000 + memory: 8000 cores: 1 nodes: 1 diff --git a/chipathlon/jobs/params/music_punctate.yaml b/chipathlon/jobs/params/music_punctate.yaml index 4e0bf45..b3a6cbc 100644 --- a/chipathlon/jobs/params/music_punctate.yaml +++ b/chipathlon/jobs/params/music_punctate.yaml @@ -84,6 +84,6 @@ music_punctate: has_value: true default: 50 walltime: 240 - memory: 16000 + memory: 8000 cores: 1 nodes: 1 diff --git a/chipathlon/jobs/params/peakranger_callpeak.yaml b/chipathlon/jobs/params/peakranger_callpeak.yaml index bab46e1..6eec39f 100644 --- a/chipathlon/jobs/params/peakranger_callpeak.yaml +++ b/chipathlon/jobs/params/peakranger_callpeak.yaml @@ -99,7 +99,7 @@ peakranger_callpeak: required: true has_value: true default: 4 - walltime: 480 - memory: 32000 + walltime: 120 + memory: 4000 cores: 4 nodes: 1 diff --git a/chipathlon/jobs/params/peakranger_format_bed.yaml b/chipathlon/jobs/params/peakranger_format_bed.yaml index 094e9e0..734afb9 100644 --- a/chipathlon/jobs/params/peakranger_format_bed.yaml +++ b/chipathlon/jobs/params/peakranger_format_bed.yaml @@ -23,6 +23,6 @@ peakranger_format_bed: has_value: true default: $outputs.0 walltime: 60 - memory: 8000 + memory: 4000 cores: 1 nodes: 1 diff --git a/chipathlon/jobs/params/picard_clean_sam.yaml b/chipathlon/jobs/params/picard_clean_sam.yaml index 9ef45a1..b81793f 100644 --- a/chipathlon/jobs/params/picard_clean_sam.yaml +++ b/chipathlon/jobs/params/picard_clean_sam.yaml @@ -28,6 +28,6 @@ picard_clean_sam: has_value: true default: $outputs.0 walltime: 60 - memory: 8000 + memory: 4000 cores: 1 nodes: 1 diff --git a/chipathlon/jobs/params/picard_mark_duplicates.yaml b/chipathlon/jobs/params/picard_mark_duplicates.yaml index cb0a758..336712e 100644 --- a/chipathlon/jobs/params/picard_mark_duplicates.yaml +++ b/chipathlon/jobs/params/picard_mark_duplicates.yaml @@ -55,7 +55,7 @@ picard_mark_duplicates: required: true has_value: true default: true - walltime: 2000 + walltime: 720 memory: 8000 cores: 1 nodes: 1 diff --git a/chipathlon/jobs/params/picard_sort_sam.yaml b/chipathlon/jobs/params/picard_sort_sam.yaml index ce6e21e..83ff014 100644 --- a/chipathlon/jobs/params/picard_sort_sam.yaml +++ b/chipathlon/jobs/params/picard_sort_sam.yaml @@ -33,7 +33,7 @@ picard_sort_sam: required: true has_value: true default: "coordinate" - walltime: 2000 + walltime: 720 memory: 8000 cores: 1 nodes: 1 diff --git a/chipathlon/jobs/params/samtools_filter_bam.yaml b/chipathlon/jobs/params/samtools_filter_bam.yaml index 82e716a..9bb32c5 100644 --- a/chipathlon/jobs/params/samtools_filter_bam.yaml +++ b/chipathlon/jobs/params/samtools_filter_bam.yaml @@ -43,7 +43,7 @@ samtools_filter_bam: changeable: false required: true has_value: false - walltime: 2000 + walltime: 60 memory: 2000 cores: 1 nodes: 1 diff --git a/chipathlon/jobs/params/samtools_remove_duplicates.yaml b/chipathlon/jobs/params/samtools_remove_duplicates.yaml index a8b739a..63a2e25 100644 --- a/chipathlon/jobs/params/samtools_remove_duplicates.yaml +++ b/chipathlon/jobs/params/samtools_remove_duplicates.yaml @@ -37,7 +37,7 @@ samtools_remove_duplicates: changeable: false required: true has_value: false - walltime: 2000 + walltime: 60 memory: 2000 cores: 1 nodes: 1 diff --git a/chipathlon/jobs/params/samtools_sam_to_bam.yaml b/chipathlon/jobs/params/samtools_sam_to_bam.yaml index 086735b..1612f1a 100644 --- a/chipathlon/jobs/params/samtools_sam_to_bam.yaml +++ b/chipathlon/jobs/params/samtools_sam_to_bam.yaml @@ -31,7 +31,7 @@ samtools_sam_to_bam: changeable: false required: true has_value: false - walltime: 2000 + walltime: 30 memory: 2000 cores: 1 nodes: 1 diff --git a/chipathlon/jobs/params/sort_awk_sort_peaks.yaml b/chipathlon/jobs/params/sort_awk_sort_peaks.yaml index 9b1b5de..0b8608d 100644 --- a/chipathlon/jobs/params/sort_awk_sort_peaks.yaml +++ b/chipathlon/jobs/params/sort_awk_sort_peaks.yaml @@ -20,7 +20,7 @@ sort_awk_sort_peaks: changeable: false required: true has_value: false - walltime: 60 + walltime: 30 memory: 4000 cores: 1 nodes: 1 diff --git a/chipathlon/jobs/params/spp_nodups_broad.yaml b/chipathlon/jobs/params/spp_nodups_broad.yaml index 8bc3e48..ae2baa4 100644 --- a/chipathlon/jobs/params/spp_nodups_broad.yaml +++ b/chipathlon/jobs/params/spp_nodups_broad.yaml @@ -87,7 +87,7 @@ spp_nodups_broad: changeable: false required: true has_value: false - walltime: 2000 + walltime: 5760 memory: 16000 cores: 8 nodes: 1 diff --git a/chipathlon/jobs/params/spp_nodups_narrow.yaml b/chipathlon/jobs/params/spp_nodups_narrow.yaml index c4e94f7..1e8e657 100644 --- a/chipathlon/jobs/params/spp_nodups_narrow.yaml +++ b/chipathlon/jobs/params/spp_nodups_narrow.yaml @@ -87,7 +87,7 @@ spp_nodups_narrow: changeable: false required: true has_value: false - walltime: 2000 + walltime: 5760 memory: 16000 cores: 8 nodes: 1 diff --git a/chipathlon/jobs/params/zcat_awk_sort_peaks.yaml b/chipathlon/jobs/params/zcat_awk_sort_peaks.yaml index ce2d88d..925353f 100644 --- a/chipathlon/jobs/params/zcat_awk_sort_peaks.yaml +++ b/chipathlon/jobs/params/zcat_awk_sort_peaks.yaml @@ -20,7 +20,7 @@ zcat_awk_sort_peaks: changeable: false required: true has_value: false - walltime: 2000 + walltime: 30 memory: 2000 cores: 1 nodes: 1 -- GitLab