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Merge pull request #356 from ENCODE-DCC/WRAN-1863_update_default_geno…
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…me_tsv_to_v4

Wran 1863 update default genome tsv to v4
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leepc12 authored Jan 6, 2022
2 parents ec036c1 + 8294aee commit 9d6ddc2
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32 changes: 14 additions & 18 deletions .circleci/config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -16,17 +16,6 @@ make_tag: &make_tag
echo "export TAG=encodedcc/atac-seq-pipeline:${CIRCLE_BRANCH}_${CIRCLE_WORKFLOW_ID}" > ${BASH_ENV}
commands:
download_task_test_data:
description: "Download task test data. This is based on py2 so run this before installing py3."
steps:
- run:
command: |
cd dev/test/test_task/
rm -rf atac-seq-pipeline-test-data
export BOTO_CONFIG=/dev/null
gsutil -m cp -r gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data .
./download_hg38_fasta_for_test_ataqc.sh

install_python3_caper_gcs:
description: "Install py3, caper and gcs. Set py3 as default python."
Expand Down Expand Up @@ -88,7 +77,7 @@ jobs:
name: build image
command: |
source ${BASH_ENV}
export DOCKER_CACHE_TAG=v1.9.3
export DOCKER_CACHE_TAG=v2.0.0
echo "pulling ${DOCKER_CACHE_TAG}!"
docker pull encodedcc/atac-seq-pipeline:${DOCKER_CACHE_TAG}
docker login -u=${DOCKERHUB_USER} -p=${DOCKERHUB_PASS}
Expand All @@ -99,7 +88,6 @@ jobs:
<<: *machine_defaults
steps:
- checkout
- download_task_test_data
- install_python3_caper_gcs
- run: *make_tag
- run:
Expand All @@ -108,6 +96,9 @@ jobs:
source ${BASH_ENV}
cd dev/test/test_task/
echo ${GCLOUD_SERVICE_ACCOUNT_SECRET_JSON} > tmp_secret_key.json
export GOOGLE_APPLICATION_CREDENTIALS=$PWD/tmp_secret_key.json
for wdl in test_*.wdl
do
prefix=${wdl%.*}
Expand All @@ -118,12 +109,17 @@ jobs:
# add docker image to input JSON
cat ${input} | jq ".+{\"${prefix}.docker\": \"${TAG}\"}" > ${input_with_docker}
caper run ${wdl} -i ${input_with_docker} -m ${metadata}
if [[ "${wdl}" != "test_choose_ctl.wdl" ]]; then
echo "Validating outputs of ${prefix}"
res=$(jq '.outputs["'${prefix}'.compare_md5sum.match_overall"]' "${metadata}")
[[ "$res" != true ]] && exit 100
if [[ "${wdl}" == test_macs2* ]]; then
# run heavy MACS2 tasks on GCP
caper run ${wdl} -i ${input_with_docker} -m ${metadata} \
--backend gcp --gcp-prj ${GOOGLE_PROJECT_ID} --docker ${TAG} \
--gcp-service-account-key-json $PWD/tmp_secret_key.json \
--out-gcs-bucket ${CAPER_OUT_DIR} --tmp-gcs-bucket ${CAPER_TMP_DIR}
else
# run other tasks locally
caper run ${wdl} -i ${input_with_docker} -m ${metadata}
fi
rm -f ${metadata}
done
Expand Down
3 changes: 2 additions & 1 deletion .gitignore
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# Byte-compiled / optimized / DLL files
# Byte-compiled / optimized / DLL files/
__pycache__/
*.py[cod]
*$py.class
Expand Down Expand Up @@ -121,4 +121,5 @@ tmp_db*
*.local.json
temp_db*
cromwell.out
cromwell.out.*
.dev
8 changes: 6 additions & 2 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,10 @@
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.156534.svg)](https://doi.org/10.5281/zenodo.156534)[![CircleCI](https://circleci.com/gh/ENCODE-DCC/atac-seq-pipeline/tree/master.svg?style=svg)](https://circleci.com/gh/ENCODE-DCC/atac-seq-pipeline/tree/master)


## Updated genome TSV files (v3 -> v4)



## Download new Caper>=2.1

New Caper is out. You need to update your Caper to work with the latest ENCODE ATAC-seq pipeline.
Expand Down Expand Up @@ -138,8 +142,8 @@ You cannot use these input JSON files directly. Go to the destination directory
We have a separate project on DNANexus to provide example FASTQs and `genome_tsv` for `hg38` and `mm10`. We recommend to make copies of these directories on your own project.

`genome_tsv`
- AWS: https://platform.dnanexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/pipeline-genome-data/genome_tsv/v3
- Azure: https://platform.dnanexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/pipeline-genome-data/genome_tsv/v3
- AWS: https://platform.dnanexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/pipeline-genome-data/genome_tsv/v4
- Azure: https://platform.dnanexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/pipeline-genome-data/genome_tsv/v4

Example FASTQs
- AWS: https://platform.dnanexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ/fastq_subsampled
Expand Down
12 changes: 6 additions & 6 deletions atac.wdl
Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,10 @@ struct RuntimeEnvironment {
}

workflow atac {
String pipeline_ver = 'v2.0.3'
String pipeline_ver = 'v2.1.0'

meta {
version: 'v2.0.3'
version: 'v2.1.0'

author: 'Jin wook Lee'
email: '[email protected]'
Expand All @@ -19,8 +19,8 @@ workflow atac {

specification_document: 'https://docs.google.com/document/d/1f0Cm4vRyDQDu0bMehHD7P7KOMxTOP-HiNoIvL1VcBt8/edit?usp=sharing'

default_docker: 'encodedcc/atac-seq-pipeline:v2.0.3'
default_singularity: 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/atac-seq-pipeline_v2.0.3.sif'
default_docker: 'encodedcc/atac-seq-pipeline:v2.1.0'
default_singularity: 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/atac-seq-pipeline_v2.1.0.sif'
default_conda: 'encode-atac-seq-pipeline'
croo_out_def: 'https://storage.googleapis.com/encode-pipeline-output-definition/atac.croo.v5.json'

Expand Down Expand Up @@ -72,8 +72,8 @@ workflow atac {
}
input {
# group: runtime_environment
String docker = 'encodedcc/atac-seq-pipeline:v2.0.3'
String singularity = 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/atac-seq-pipeline_v2.0.3.sif'
String docker = 'encodedcc/atac-seq-pipeline:v2.1.0'
String singularity = 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/atac-seq-pipeline_v2.1.0.sif'
String conda = 'encode-atac-seq-pipeline'
String conda_macs2 = 'encode-atac-seq-pipeline-macs2'
String conda_spp = 'encode-atac-seq-pipeline-spp'
Expand Down
28 changes: 26 additions & 2 deletions dev/test/test_task/compare_md5sum.wdl
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,13 @@ task compare_md5sum {
import os
import json
import hashlib
import struct
def getuncompressedsize(filename):
# https://stackoverflow.com/a/22348071
with open(filename, 'rb') as f:
f.seek(-4, 2)
return struct.unpack('I', f.read(4))[0]
def md5sum(filename, blocksize=65536):
hash = hashlib.md5()
Expand Down Expand Up @@ -39,16 +46,33 @@ task compare_md5sum {
ref_f = ref_files[i]
md5 = md5sum(f)
ref_md5 = md5sum(ref_f)
filesize = os.path.getsize(f)
ref_filesize = os.path.getsize(ref_f)
# if text file, read in contents
if f.endswith('.qc') or f.endswith('.txt') or \
f.endswith('.log') or f.endswith('.out'):
with open(f,'r') as fp:
contents = fp.read()
with open(ref_f,'r') as fp:
ref_contents = fp.read()
elif f.endswith('.gz'):
uncompressed_filesize = getuncompressedsize(f)
ref_uncompressed_filesize = getuncompressedsize(ref_f)
contents = 'filesize={filesize}, uncompressed_filesize={uncompressed_filesize}'.format(
filesize=filesize,
uncompressed_filesize=uncompressed_filesize,
)
ref_contents = 'filesize={filesize}, uncompressed_filesize={uncompressed_filesize}'.format(
filesize=ref_filesize,
uncompressed_filesize=ref_uncompressed_filesize,
)
else:
contents = ''
ref_contents = ''
contents = 'filesize={filesize}'.format(filesize=filesize)
ref_contents = 'filesize={filesize}'.format(filesize=ref_filesize)
matched = md5==ref_md5
result['tasks'].append(OrderedDict([
('label', label),
Expand Down
4 changes: 0 additions & 4 deletions dev/test/test_task/download_hg38_fasta_for_test_ataqc.sh

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12 changes: 6 additions & 6 deletions dev/test/test_task/test_annot_enrich.json
Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
{
"test_annot_enrich.blacklist" : "atac-seq-pipeline-test-data/genome_data/hg38_chr19_chrM/hg38.blacklist.bed.gz",
"test_annot_enrich.dnase" : "atac-seq-pipeline-test-data/genome_data/hg38/ataqc/reg2map_honeybadger2_dnase_all_p10_ucsc.hg19_to_hg38.bed.gz",
"test_annot_enrich.prom" : "atac-seq-pipeline-test-data/genome_data/hg38/ataqc/reg2map_honeybadger2_dnase_prom_p2.hg19_to_hg38.bed.gz",
"test_annot_enrich.enh" : "atac-seq-pipeline-test-data/genome_data/hg38/ataqc/reg2map_honeybadger2_dnase_enh_p2.hg19_to_hg38.bed.gz",
"test_annot_enrich.blacklist" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/genome_data/hg38_chr19_chrM/hg38.blacklist.bed.gz",
"test_annot_enrich.dnase" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/genome_data/hg38/ataqc/reg2map_honeybadger2_dnase_all_p10_ucsc.hg19_to_hg38.bed.gz",
"test_annot_enrich.prom" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/genome_data/hg38/ataqc/reg2map_honeybadger2_dnase_prom_p2.hg19_to_hg38.bed.gz",
"test_annot_enrich.enh" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/genome_data/hg38/ataqc/reg2map_honeybadger2_dnase_enh_p2.hg19_to_hg38.bed.gz",

"test_annot_enrich.ta" : "atac-seq-pipeline-test-data/input/pe/ataqc/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz",
"test_annot_enrich.ta" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/input/pe/ataqc/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz",

"test_annot_enrich.ref_annot_enrich_qc" : "atac-seq-pipeline-test-data/ref_output/test_annot_enrich/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.annot_enrich.qc"
"test_annot_enrich.ref_annot_enrich_qc" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/ref_output/test_annot_enrich/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.annot_enrich.qc"
}
16 changes: 8 additions & 8 deletions dev/test/test_task/test_bam2ta.json
Original file line number Diff line number Diff line change
@@ -1,14 +1,14 @@
{
"test_bam2ta.pe_nodup_bam" : "atac-seq-pipeline-test-data/input/pe/nodup_bams/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.bam",
"test_bam2ta.se_nodup_bam" : "atac-seq-pipeline-test-data/input/se/nodup_bams/rep1/ENCFF439VSY.subsampled.400.trim.merged.nodup.bam",
"test_bam2ta.pe_nodup_bam" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/input/pe/nodup_bams/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.bam",
"test_bam2ta.se_nodup_bam" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/input/se/nodup_bams/rep1/ENCFF439VSY.subsampled.400.trim.merged.nodup.bam",

"test_bam2ta.ref_pe_ta" : "atac-seq-pipeline-test-data/ref_output/test_bam2ta/pe/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz",
"test_bam2ta.ref_pe_ta_disable_tn5_shift" : "atac-seq-pipeline-test-data/ref_output/test_bam2ta/pe/disable_tn5_shift/ENCFF341MYG.subsampled.400.trim.merged.nodup.tagAlign.gz",
"test_bam2ta.ref_pe_ta_subsample" : "atac-seq-pipeline-test-data/ref_output/test_bam2ta/pe/subsample/fix_PIP-917/ENCFF341MYG.subsampled.400.trim.merged.nodup.5K.tn5.tagAlign.gz",
"test_bam2ta.ref_pe_ta" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/ref_output/test_bam2ta/pe/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz",
"test_bam2ta.ref_pe_ta_disable_tn5_shift" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/ref_output/test_bam2ta/pe/disable_tn5_shift/ENCFF341MYG.subsampled.400.trim.merged.nodup.tagAlign.gz",
"test_bam2ta.ref_pe_ta_subsample" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/ref_output/test_bam2ta/pe/subsample/fix_PIP-917/ENCFF341MYG.subsampled.400.trim.merged.nodup.5K.tn5.tagAlign.gz",

"test_bam2ta.ref_se_ta" : "atac-seq-pipeline-test-data/ref_output/test_bam2ta/se/ENCFF439VSY.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz",
"test_bam2ta.ref_se_ta_disable_tn5_shift" : "atac-seq-pipeline-test-data/ref_output/test_bam2ta/se/disable_tn5_shift/ENCFF439VSY.subsampled.400.trim.merged.nodup.tagAlign.gz",
"test_bam2ta.ref_se_ta_subsample" : "atac-seq-pipeline-test-data/ref_output/test_bam2ta/se/subsample/ENCFF439VSY.subsampled.400.trim.merged.nodup.5K.tn5.tagAlign.gz",
"test_bam2ta.ref_se_ta" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/ref_output/test_bam2ta/se/ENCFF439VSY.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz",
"test_bam2ta.ref_se_ta_disable_tn5_shift" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/ref_output/test_bam2ta/se/disable_tn5_shift/ENCFF439VSY.subsampled.400.trim.merged.nodup.tagAlign.gz",
"test_bam2ta.ref_se_ta_subsample" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/ref_output/test_bam2ta/se/subsample/ENCFF439VSY.subsampled.400.trim.merged.nodup.5K.tn5.tagAlign.gz",

"test_bam2ta.bam2ta_subsample" : 5000
}
32 changes: 16 additions & 16 deletions dev/test/test_task/test_bowtie2.json
Original file line number Diff line number Diff line change
@@ -1,28 +1,28 @@
{
"test_bowtie2.pe_fastqs_R1" : [
"atac-seq-pipeline-test-data/input/pe/fastqs/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz",
"atac-seq-pipeline-test-data/input/pe/fastqs/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz"
"gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/input/pe/fastqs/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz",
"gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/input/pe/fastqs/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz"
],
"test_bowtie2.pe_fastqs_R2" : [
"atac-seq-pipeline-test-data/input/pe/fastqs/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz",
"atac-seq-pipeline-test-data/input/pe/fastqs/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz"
"gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/input/pe/fastqs/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz",
"gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/input/pe/fastqs/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz"
],
"test_bowtie2.se_fastqs_R1" : [
"atac-seq-pipeline-test-data/input/se/fastqs/rep1/ENCFF439VSY.subsampled.400.fastq.gz",
"atac-seq-pipeline-test-data/input/se/fastqs/rep1/ENCFF325FCQ.subsampled.400.fastq.gz",
"atac-seq-pipeline-test-data/input/se/fastqs/rep1/ENCFF683IQS.subsampled.400.fastq.gz",
"atac-seq-pipeline-test-data/input/se/fastqs/rep1/ENCFF744CHW.subsampled.400.fastq.gz"
"gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/input/se/fastqs/rep1/ENCFF439VSY.subsampled.400.fastq.gz",
"gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/input/se/fastqs/rep1/ENCFF325FCQ.subsampled.400.fastq.gz",
"gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/input/se/fastqs/rep1/ENCFF683IQS.subsampled.400.fastq.gz",
"gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/input/se/fastqs/rep1/ENCFF744CHW.subsampled.400.fastq.gz"
],
"test_bowtie2.pe_bowtie2_idx_tar" : "atac-seq-pipeline-test-data/genome_data/hg38_chr19_chrM/bowtie2_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta.tar",
"test_bowtie2.se_bowtie2_idx_tar" : "atac-seq-pipeline-test-data/genome_data/mm10_chr19_chrM/bowtie2_index/mm10_no_alt_analysis_set_ENCODE.chr19_chrM.fasta.tar",
"test_bowtie2.pe_bowtie2_idx_tar" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/genome_data/hg38_chr19_chrM/bowtie2_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta.tar",
"test_bowtie2.se_bowtie2_idx_tar" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/genome_data/mm10_chr19_chrM/bowtie2_index/mm10_no_alt_analysis_set_ENCODE.chr19_chrM.fasta.tar",

"test_bowtie2.se_chrsz" : "atac-seq-pipeline-test-data/genome_data/mm10_chr19_chrM/mm10_chr19_chrM.chrom.sizes",
"test_bowtie2.pe_chrsz" : "atac-seq-pipeline-test-data/genome_data/hg38_chr19_chrM/hg38_chr19_chrM.chrom.sizes",
"test_bowtie2.se_chrsz" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/genome_data/mm10_chr19_chrM/mm10_chr19_chrM.chrom.sizes",
"test_bowtie2.pe_chrsz" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/genome_data/hg38_chr19_chrM/hg38_chr19_chrM.chrom.sizes",

"test_bowtie2.ref_pe_flagstat" : "atac-seq-pipeline-test-data/ref_output/test_bowtie2/pe/multimapping/merge_fastqs_R1_ENCFF341MYG.subsampled.400.trim.merged.samstats.qc",
"test_bowtie2.ref_pe_flagstat_no_multimapping" : "atac-seq-pipeline-test-data/ref_output/test_bowtie2/pe/no_multimapping/merge_fastqs_R1_ENCFF341MYG.subsampled.400.trim.merged.samstats.qc",
"test_bowtie2.ref_se_flagstat" : "atac-seq-pipeline-test-data/ref_output/test_bowtie2/se/multimapping/merge_fastqs_R1_ENCFF439VSY.subsampled.400.trim.merged.samstats.qc",
"test_bowtie2.ref_se_flagstat_no_multimapping" : "atac-seq-pipeline-test-data/ref_output/test_bowtie2/se/no_multimapping/merge_fastqs_R1_ENCFF439VSY.subsampled.400.trim.merged.samstats.qc",
"test_bowtie2.ref_pe_flagstat" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/ref_output/test_bowtie2/pe/multimapping/merge_fastqs_R1_ENCFF341MYG.subsampled.400.trim.merged.samstats.qc",
"test_bowtie2.ref_pe_flagstat_no_multimapping" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/ref_output/test_bowtie2/pe/no_multimapping/merge_fastqs_R1_ENCFF341MYG.subsampled.400.trim.merged.samstats.qc",
"test_bowtie2.ref_se_flagstat" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/ref_output/test_bowtie2/se/multimapping/merge_fastqs_R1_ENCFF439VSY.subsampled.400.trim.merged.samstats.qc",
"test_bowtie2.ref_se_flagstat_no_multimapping" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/ref_output/test_bowtie2/se/no_multimapping/merge_fastqs_R1_ENCFF439VSY.subsampled.400.trim.merged.samstats.qc",

"test_bowtie2.multimapping" : 4
}
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