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@leepc12
leepc12 committed Oct 30, 2020
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60 changes: 60 additions & 0 deletions chip.croo.v5.json
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Original file line number Diff line number Diff line change
Expand Up @@ -177,6 +177,10 @@
"path": "peak/rep${i+1}/${basename}",
"table": "Peak/Replicate ${i+1}/Blacklist-filtered narrowpeak (BigBed)"
},
"bfilt_peak_starch": {
"path": "peak/rep${i+1}/${basename}",
"table": "Peak/Replicate ${i+1}/Blacklist-filtered narrowpeak (starch)"
},
"bfilt_peak_hammock": {
"path": "peak/rep${i+1}/${basename}",
"table": "Peak/Replicate ${i+1}/Blacklist-filtered narrowpeak (hammock)"
Expand All @@ -199,6 +203,10 @@
"path": "peak/rep${i+1}/pseudorep1/${basename}",
"table": "Peak/Replicate ${i+1}/Pseudoreplicate 1/Blacklist-filtered narrowpeak (BigBed)"
},
"bfilt_peak_starch": {
"path": "peak/rep${i+1}/pseudorep1/${basename}",
"table": "Peak/Replicate ${i+1}/Pseudoreplicate 1/Blacklist-filtered narrowpeak (starch)"
},
"bfilt_peak_hammock": {
"path": "peak/rep${i+1}/pseudorep1/${basename}",
"table": "Peak/Replicate ${i+1}/Pseudoreplicate 1/Blacklist-filtered narrowpeak (hammock)"
Expand All @@ -221,6 +229,10 @@
"path": "peak/rep${i+1}/pseudorep2/${basename}",
"table": "Peak/Replicate ${i+1}/Pseudoreplicate 2/Blacklist-filtered narrowpeak (BigBed)"
},
"bfilt_peak_starch": {
"path": "peak/rep${i+1}/pseudorep2/${basename}",
"table": "Peak/Replicate ${i+1}/Pseudoreplicate 2/Blacklist-filtered narrowpeak (starch)"
},
"bfilt_peak_hammock": {
"path": "peak/rep${i+1}/pseudorep2/${basename}",
"table": "Peak/Replicate ${i+1}/Pseudoreplicate 2/Blacklist-filtered narrowpeak (hammock)"
Expand All @@ -247,6 +259,10 @@
"path": "peak/pooled-rep/${basename}",
"table": "Peak/Pooled replicate/Blacklist-filtered narrowpeak (BigBed)"
},
"bfilt_peak_starch": {
"path": "peak/pooled-rep/${basename}",
"table": "Peak/Pooled replicate/Blacklist-filtered narrowpeak (starch)"
},
"bfilt_peak_hammock": {
"path": "peak/pooled-rep/${basename}",
"table": "Peak/Pooled replicate/Blacklist-filtered narrowpeak (hammock)"
Expand All @@ -269,6 +285,10 @@
"path": "peak/pooled-rep/pseudorep1/${basename}",
"table": "Peak/Pooled replicate/Pseudoreplicate 1/Blacklist-filtered narrowpeak (BigBed)"
},
"bfilt_peak_starch": {
"path": "peak/pooled-rep/pseudorep1/${basename}",
"table": "Peak/Pooled replicate/Pseudoreplicate 1/Blacklist-filtered narrowpeak (starch)"
},
"bfilt_peak_hammock": {
"path": "peak/pooled-rep/pseudorep1/${basename}",
"table": "Peak/Pooled replicate/Pseudoreplicate 1/Blacklist-filtered narrowpeak (hammock)"
Expand All @@ -291,6 +311,10 @@
"path": "peak/pooled-rep/pseudorep2/${basename}",
"table": "Peak/Pooled replicate/Pseudoreplicate 2/Blacklist-filtered narrowpeak (BigBed)"
},
"bfilt_peak_starch": {
"path": "peak/pooled-rep/pseudorep2/${basename}",
"table": "Peak/Pooled replicate/Pseudoreplicate 2/Blacklist-filtered narrowpeak (starch)"
},
"bfilt_peak_hammock": {
"path": "peak/pooled-rep/pseudorep2/${basename}",
"table": "Peak/Pooled replicate/Pseudoreplicate 2/Blacklist-filtered narrowpeak (hammock)"
Expand Down Expand Up @@ -370,6 +394,10 @@
"path": "peak/${basename.split('.')[0].replace('_vs_','_').replace('_','_vs_').replace('-','_vs_')}/${basename}",
"table": "Peak/${basename.split('.')[0].replace('_vs_','_').replace('_',' vs. ').replace('-',' vs. ').capitalize()}/Blacklist-filtered IDR peak (BigBed)"
},
"bfilt_idr_peak_starch": {
"path": "peak/${basename.split('.')[0].replace('_vs_','_').replace('_','_vs_').replace('-','_vs_')}/${basename}",
"table": "Peak/${basename.split('.')[0].replace('_vs_','_').replace('_',' vs. ').replace('-',' vs. ').capitalize()}/Blacklist-filtered IDR peak (starch)"
},
"bfilt_idr_peak_hammock": {
"path": "peak/${basename.split('.')[0].replace('_vs_','_').replace('_','_vs_').replace('-','_vs_')}/${basename}",
"table": "Peak/${basename.split('.')[0].replace('_vs_','_').replace('_',' vs. ').replace('-',' vs. ').capitalize()}/Blacklist-filtered IDR peak (hammock)"
Expand Down Expand Up @@ -402,6 +430,10 @@
"path": "peak/pooled-pseudorep1_vs_2/${basename}",
"table": "Peak/Pooled pseudoreplicate 1 vs. 2/Blacklist-filtered IDR peak (BigBed)"
},
"bfilt_idr_peak_starch": {
"path": "peak/pooled-pseudorep1_vs_2/${basename}",
"table": "Peak/Pooled pseudoreplicate 1 vs. 2/Blacklist-filtered IDR peak (starch)"
},
"bfilt_idr_peak_hammock": {
"path": "peak/pooled-pseudorep1_vs_2/${basename}",
"table": "Peak/Pooled pseudoreplicate 1 vs. 2/Blacklist-filtered IDR peak (hammock)"
Expand Down Expand Up @@ -433,6 +465,10 @@
"path": "peak/rep${i+1}-pseudorep1_vs_2/${basename}",
"table": "Peak/Replicate ${i+1}/Pseudorep 1 vs. pseudorep 2/Blacklist-filtered IDR peak (BigBed)"
},
"bfilt_idr_peak_starch": {
"path": "peak/rep${i+1}-pseudorep1_vs_2/${basename}",
"table": "Peak/Replicate ${i+1}/Pseudorep 1 vs. pseudorep 2/Blacklist-filtered IDR peak (starch)"
},
"bfilt_idr_peak_hammock": {
"path": "peak/rep${i+1}-pseudorep1_vs_2/${basename}",
"table": "Peak/Replicate ${i+1}/Pseudorep 1 vs. pseudorep 2/Blacklist-filtered IDR peak (hammock)"
Expand Down Expand Up @@ -464,6 +500,10 @@
"path": "peak/${basename.split('.')[0].replace('_vs_','_').replace('_','_vs_').replace('-','_vs_')}/${basename}",
"table": "Peak/${basename.split('.')[0].replace('_vs_','_').replace('_',' vs. ').replace('-',' vs. ').capitalize()}/Blacklist-filtered overlap peak (BigBed)"
},
"bfilt_overlap_peak_starch": {
"path": "peak/${basename.split('.')[0].replace('_vs_','_').replace('_','_vs_').replace('-','_vs_')}/${basename}",
"table": "Peak/${basename.split('.')[0].replace('_vs_','_').replace('_',' vs. ').replace('-',' vs. ').capitalize()}/Blacklist-filtered overlap peak (starch)"
},
"bfilt_overlap_peak_hammock": {
"path": "peak/${basename.split('.')[0].replace('_vs_','_').replace('_','_vs_').replace('-','_vs_')}/${basename}",
"table": "Peak/${basename.split('.')[0].replace('_vs_','_').replace('_',' vs. ').replace('-',' vs. ').capitalize()}/Blacklist-filtered overlap peak (hammock)"
Expand All @@ -483,6 +523,10 @@
"path": "peak/pooled-pseudorep1_vs_2/${basename}",
"table": "Peak/Pooled pseudoreplicate 1 vs. 2/Blacklist-filtered overlap peak (BigBed)"
},
"bfilt_overlap_peak_starch": {
"path": "peak/pooled-pseudorep1_vs_2/${basename}",
"table": "Peak/Pooled pseudoreplicate 1 vs. 2/Blacklist-filtered overlap peak (starch)"
},
"bfilt_overlap_peak_hammock": {
"path": "peak/pooled-pseudorep1_vs_2/${basename}",
"table": "Peak/Pooled pseudoreplicate 1 vs. 2/Blacklist-filtered overlap peak (hammock)"
Expand All @@ -501,6 +545,10 @@
"path": "peak/rep${i+1}-pseudorep1_vs_2/${basename}",
"table": "Peak/Replicate ${i+1}/Pseudorep 1 vs. pseudorep 2/Blacklist-filtered overlap peak (BigBed)"
},
"bfilt_overlap_peak_starch": {
"path": "peak/rep${i+1}-pseudorep1_vs_2/${basename}",
"table": "Peak/Replicate ${i+1}/Pseudorep 1 vs. pseudorep 2/Blacklist-filtered overlap peak (starch)"
},
"bfilt_overlap_peak_hammock": {
"path": "peak/rep${i+1}-pseudorep1_vs_2/${basename}",
"table": "Peak/Replicate ${i+1}/Pseudorep 1 vs. pseudorep 2/Blacklist-filtered overlap peak (hammock)"
Expand All @@ -521,6 +569,10 @@
"table": "Peak/IDR reproducibility/Optimal peak (BigBed)",
"ucsc_track": "track type=bigBed name=\"Optimal IDR peak\" priority=100 color=0,0,255 visibility=full"
},
"optimal_peak_starch": {
"path": "peak/idr_reproducibility/${basename}",
"table": "Peak/IDR reproducibility/Optimal peak (starch)"
},
"optimal_peak_hammock": {
"path": "peak/idr_reproducibility/${basename}",
"table": "Peak/IDR reproducibility/Optimal peak (hammock)"
Expand All @@ -534,6 +586,10 @@
"table": "Peak/IDR reproducibility/Conservative peak (BigBed)",
"ucsc_track": "track type=bigBed name=\"Conservative IDR peak\" priority=100 color=0,0,255 visibility=full"
},
"conservative_peak_starch": {
"path": "peak/idr_reproducibility/${basename}",
"table": "Peak/IDR reproducibility/Conservative peak (starch)"
},
"conservative_peak_hammock": {
"path": "peak/idr_reproducibility/${basename}",
"table": "Peak/IDR reproducibility/Conservative peak (hammock)"
Expand Down Expand Up @@ -568,6 +624,10 @@
"table": "Peak/Overlap reproducibility/Conservative peak (BigBed)",
"ucsc_track": "track type=bigBed name=\"Conservative overlap peak\" priority=100 color=0,0,255 visibility=full"
},
"conservative_peak_starch": {
"path": "peak/overlap_reproducibility/${basename}",
"table": "Peak/Overlap reproducibility/Conservative peak (starch)"
},
"conservative_peak_hammock": {
"path": "peak/overlap_reproducibility/${basename}",
"table": "Peak/Overlap reproducibility/Conservative peak (hammock)"
Expand Down
7 changes: 6 additions & 1 deletion chip.wdl
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Expand Up @@ -10,7 +10,7 @@ workflow chip {

caper_docker: 'encodedcc/chip-seq-pipeline:v1.6.1'
caper_singularity: 'docker://encodedcc/chip-seq-pipeline:v1.6.1'
croo_out_def: 'https://storage.googleapis.com/encode-pipeline-output-definition/chip.croo.v4.json'
croo_out_def: 'https://storage.googleapis.com/encode-pipeline-output-definition/chip.croo.v5.json'

parameter_group: {
pipeline_metadata: {
Expand Down Expand Up @@ -2507,6 +2507,7 @@ task call_peak {
# generated by post_call_peak py
File bfilt_peak = glob('*.bfilt.'+peak_type+'.gz')[0]
File bfilt_peak_bb = glob('*.bfilt.'+peak_type+'.bb')[0]
File bfilt_peak_starch = glob('*.bfilt.'+peak_type+'.starch')[0]
File bfilt_peak_hammock = glob('*.bfilt.'+peak_type+'.hammock.gz*')[0]
File bfilt_peak_hammock_tbi = glob('*.bfilt.'+peak_type+'.hammock.gz*')[1]
File frip_qc = glob('*.frip.qc')[0]
Expand Down Expand Up @@ -2599,6 +2600,7 @@ task idr {
File idr_peak = glob('*[!.][!b][!f][!i][!l][!t].'+peak_type+'.gz')[0]
File bfilt_idr_peak = glob('*.bfilt.'+peak_type+'.gz')[0]
File bfilt_idr_peak_bb = glob('*.bfilt.'+peak_type+'.bb')[0]
File bfilt_idr_peak_starch = glob('*.bfilt.'+peak_type+'.starch')[0]
File bfilt_idr_peak_hammock = glob('*.bfilt.'+peak_type+'.hammock.gz*')[0]
File bfilt_idr_peak_hammock_tbi = glob('*.bfilt.'+peak_type+'.hammock.gz*')[1]
File idr_plot = glob('*.txt.png')[0]
Expand Down Expand Up @@ -2648,6 +2650,7 @@ task overlap {
File overlap_peak = glob('*[!.][!b][!f][!i][!l][!t].'+peak_type+'.gz')[0]
File bfilt_overlap_peak = glob('*.bfilt.'+peak_type+'.gz')[0]
File bfilt_overlap_peak_bb = glob('*.bfilt.'+peak_type+'.bb')[0]
File bfilt_overlap_peak_starch = glob('*.bfilt.'+peak_type+'.starch')[0]
File bfilt_overlap_peak_hammock = glob('*.bfilt.'+peak_type+'.hammock.gz*')[0]
File bfilt_overlap_peak_hammock_tbi = glob('*.bfilt.'+peak_type+'.hammock.gz*')[1]
File frip_qc = if defined(ta) then glob('*.frip.qc')[0] else glob('null')[0]
Expand Down Expand Up @@ -2686,10 +2689,12 @@ task reproducibility {
output {
File optimal_peak = glob('*optimal_peak.*.gz')[0]
File optimal_peak_bb = glob('*optimal_peak.*.bb')[0]
File optimal_peak_starch = glob('*optimal_peak.*.starch')[0]
File optimal_peak_hammock = glob('*optimal_peak.*.hammock.gz*')[0]
File optimal_peak_hammock_tbi = glob('*optimal_peak.*.hammock.gz*')[1]
File conservative_peak = glob('*conservative_peak.*.gz')[0]
File conservative_peak_bb = glob('*conservative_peak.*.bb')[0]
File conservative_peak_starch = glob('*conservative_peak.*.starch')[0]
File conservative_peak_hammock = glob('*conservative_peak.*.hammock.gz*')[0]
File conservative_peak_hammock_tbi = glob('*conservative_peak.*.hammock.gz*')[1]
File reproducibility_qc = glob('*reproducibility.qc')[0]
Expand Down
4 changes: 4 additions & 0 deletions dev/docker_image/Dockerfile
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Expand Up @@ -111,6 +111,10 @@ RUN wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmoma
# Install pytest for testing environment
RUN pip3 install --no-cache-dir pytest

# Install bedops 2.4.39
RUN mkdir bedops_2.4.39 && cd bedops_2.4.39 && wget https://github.com/bedops/bedops/releases/download/v2.4.39/bedops_linux_x86_64-v2.4.39.tar.bz2 && tar -xvjf bedops_linux_x86_64-v2.4.39.tar.bz2 && rm -f bedops_linux_x86_64-v2.4.39.tar.bz2
ENV PATH="/software/bedops_2.4.39/bin:${PATH}"

# Prevent conflict with locally installed python outside of singularity container
ENV PYTHONNOUSERSITE=True

Expand Down
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