Merge pull request #264 from ENCODE-DCC/dev

v2.1.4

.circleci/config.yml

@@ -7,7 +7,7 @@ defaults: &defaults
 
 machine_defaults: &machine_defaults
  machine: 
- image: ubuntu-1604:202007-01
+ image: ubuntu-2004:202010-01
  working_directory: ~/chip-seq-pipeline2
 
 make_tag: &make_tag
@@ -16,37 +16,17 @@ make_tag: &make_tag
  echo "export TAG=encodedcc/chip-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 chip-seq-pipeline-test-data
- export BOTO_CONFIG=/dev/null
- gsutil -m cp -r gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data .
-
  install_python3_caper_gcs:
  description: "Install py3, caper and gcs. Set py3 as default python."
  steps: 
  - run:
  command: |
  sudo apt-get update && sudo apt-get install software-properties-common git wget curl -y
+ sudo apt-get install -y software-properties-common git wget curl python3 python3-pip default-jre
 
- # install java 11
- sudo add-apt-repository ppa:openjdk-r/ppa -y
- sudo apt-get update && sudo apt-get install openjdk-11-jdk -y
- # automatically set 11 as default java
- sudo update-java-alternatives -a
-
- sudo add-apt-repository ppa:deadsnakes/ppa -y
- sudo apt-get update && sudo apt-get install python3.6 -y
- sudo wget --no-check-certificate https://bootstrap.pypa.io/get-pip.py
- sudo python3.6 get-pip.py
- sudo ln -s /usr/bin/python3.6 /usr/local/bin/python3
-
- pip3 install --upgrade pip
- pip3 install caper google-cloud-storage
+ sudo python3 -m pip install --upgrade pip
+ sudo pip3 install PyYAML --ignore-installed
+ sudo pip3 install caper google-cloud-storage
 
  run_workflow_test:
  description: "Run workflow test. This requires an env var INPUT as input JSON's basename."
@@ -86,7 +66,7 @@ jobs:
  name: build image
  command: |
  source ${BASH_ENV}
- export DOCKER_CACHE_TAG=v1.8.1
+ export DOCKER_CACHE_TAG=v2.1.0
  echo "pulling ${DOCKER_CACHE_TAG}!"
  docker pull encodedcc/chip-seq-pipeline:${DOCKER_CACHE_TAG}
  docker login -u=${DOCKERHUB_USER} -p=${DOCKERHUB_PASS}
@@ -97,7 +77,6 @@ jobs:
  <<: *machine_defaults
  steps:
  - checkout
- - download_task_test_data
  - install_python3_caper_gcs
  - run: *make_tag
  - run:
@@ -106,6 +85,9 @@ 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
+
  # unittest for wrapper .py
  docker run ${TAG} bash -c "cd /software/chip-seq-pipeline/dev/test/test_py/; pytest -vv"
 

.gitignore

@@ -125,3 +125,5 @@ tmp_db*
 temp_db*
 
 cromwell.out
+cromwell.out.*
+

README.md

@@ -127,8 +127,8 @@ 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` (also chr19-only version of those two. Use chr19-only versions for testing). 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-chip-seq-pipeline/ENCSR000DYI/fastq_subsampled

chip.wdl

@@ -7,10 +7,10 @@ struct RuntimeEnvironment {
 }
 
 workflow chip {
- String pipeline_ver = 'v2.1.2'
+ String pipeline_ver = 'v2.1.4'
 
  meta {
- version: 'v2.1.2'
+ version: 'v2.1.4'
 
  author: 'Jin wook Lee'
  email: 'leepc12@gmail.com'
@@ -19,8 +19,8 @@ workflow chip {
 
  specification_document: 'https://docs.google.com/document/d/1lG_Rd7fnYgRpSIqrIfuVlAz2dW1VaSQThzk836Db99c/edit?usp=sharing'
 
- default_docker: 'encodedcc/chip-seq-pipeline:v2.1.2'
- default_singularity: 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/chip-seq-pipeline_v2.1.2.sif'
+ default_docker: 'encodedcc/chip-seq-pipeline:v2.1.4'
+ default_singularity: 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/chip-seq-pipeline_v2.1.4.sif'
  croo_out_def: 'https://storage.googleapis.com/encode-pipeline-output-definition/chip.croo.v5.json'
 
  parameter_group: {
@@ -71,8 +71,8 @@ workflow chip {
  }
  input {
  # group: runtime_environment
- String docker = 'encodedcc/chip-seq-pipeline:v2.1.2'
- String singularity = 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/chip-seq-pipeline_v2.1.2.sif'
+ String docker = 'encodedcc/chip-seq-pipeline:v2.1.4'
+ String singularity = 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/chip-seq-pipeline_v2.1.4.sif'
  String conda = 'encode-chip-seq-pipeline'
  String conda_macs2 = 'encode-chip-seq-pipeline-macs2'
  String conda_spp = 'encode-chip-seq-pipeline-spp'
@@ -2096,6 +2096,7 @@ workflow chip {
  ctl_paired_ends = ctl_paired_end_,
  pipeline_type = pipeline_type,
  aligner = aligner_,
+ no_dup_removal = no_dup_removal,
  peak_caller = peak_caller_,
  cap_num_peak = cap_num_peak_,
  idr_thresh = idr_thresh,
@@ -3046,6 +3047,7 @@ task qc_report {
  Array[Boolean] ctl_paired_ends
  String pipeline_type
  String aligner
+ Boolean no_dup_removal
  String peak_caller
  Int cap_num_peak
  Float idr_thresh
@@ -3105,6 +3107,7 @@ task qc_report {
  command {
  set -e
  python3 $(which encode_task_qc_report.py) \
+ --pipeline-prefix chip \
  ${'--pipeline-ver ' + pipeline_ver} \
  ${"--title '" + sub(title,"'","_") + "'"} \
  ${"--desc '" + sub(description,"'","_") + "'"} \
@@ -3114,6 +3117,7 @@ task qc_report {
  --ctl-paired-ends ${sep=' ' ctl_paired_ends} \
  --pipeline-type ${pipeline_type} \
  --aligner ${aligner} \
+ ${if (no_dup_removal) then '--no-dup-removal ' else ''} \
  --peak-caller ${peak_caller} \
  ${'--cap-num-peak ' + cap_num_peak} \
  --idr-thresh ${idr_thresh} \

dev/test/test_task/test_bam2ta.json

@@ -1,12 +1,12 @@
 {
- "test_bam2ta.pe_nodup_bam" : "chip-seq-pipeline-test-data/input/pe/nodup_bams/rep1/rep1-R1.subsampled.67.merged.nodup.bam",
- "test_bam2ta.se_nodup_bam" : "chip-seq-pipeline-test-data/input/se/nodup_bams/rep1/rep1.subsampled.25.merged.nodup.bam",
+ "test_bam2ta.pe_nodup_bam" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/input/pe/nodup_bams/rep1/rep1-R1.subsampled.67.merged.nodup.bam",
+ "test_bam2ta.se_nodup_bam" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/input/se/nodup_bams/rep1/rep1.subsampled.25.merged.nodup.bam",
 
- "test_bam2ta.ref_pe_ta" : "chip-seq-pipeline-test-data/ref_output/test_bam2ta/pe/rep1-R1.subsampled.67.merged.nodup.tagAlign.gz",
- "test_bam2ta.ref_pe_ta_subsample" : "chip-seq-pipeline-test-data/ref_output/test_bam2ta/pe/subsample/fix_PIP-917/rep1-R1.subsampled.67.merged.nodup.17K.tagAlign.gz",
+ "test_bam2ta.ref_pe_ta" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/ref_output/test_bam2ta/pe/rep1-R1.subsampled.67.merged.nodup.tagAlign.gz",
+ "test_bam2ta.ref_pe_ta_subsample" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/ref_output/test_bam2ta/pe/subsample/fix_PIP-917/rep1-R1.subsampled.67.merged.nodup.17K.tagAlign.gz",
 
- "test_bam2ta.ref_se_ta" : "chip-seq-pipeline-test-data/ref_output/test_bam2ta/se/rep1.subsampled.25.merged.nodup.tagAlign.gz",
- "test_bam2ta.ref_se_ta_subsample" : "chip-seq-pipeline-test-data/ref_output/test_bam2ta/se/subsample/rep1.subsampled.25.merged.nodup.17K.tagAlign.gz",
+ "test_bam2ta.ref_se_ta" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/ref_output/test_bam2ta/se/rep1.subsampled.25.merged.nodup.tagAlign.gz",
+ "test_bam2ta.ref_se_ta_subsample" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/ref_output/test_bam2ta/se/subsample/rep1.subsampled.25.merged.nodup.17K.tagAlign.gz",
 
  "test_bam2ta.bam2ta_subsample" : 17000
 }

dev/test/test_task/test_bam_to_pbam.json

@@ -1,9 +1,9 @@
 {
- "test_bam_to_pbam.ref_fa" : "chip-seq-pipeline-test-data/genome_data/hg38_chr19_chrM/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta.gz",
- "test_bam_to_pbam.chrsz" : "chip-seq-pipeline-test-data/genome_data/hg38_chr19_chrM/hg38_chr19_chrM.chrom.sizes",
- "test_bam_to_pbam.pe_bam" : "chip-seq-pipeline-test-data/input/pe/bams/rep1/rep1-R1.subsampled.67.merged.bam",
- "test_bam_to_pbam.se_bam" : "chip-seq-pipeline-test-data/input/se/bams/rep1/rep1.subsampled.25.merged.bam",
+ "test_bam_to_pbam.ref_fa" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/genome_data/hg38_chr19_chrM/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta.gz",
+ "test_bam_to_pbam.chrsz" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/genome_data/hg38_chr19_chrM/hg38_chr19_chrM.chrom.sizes",
+ "test_bam_to_pbam.pe_bam" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/input/pe/bams/rep1/rep1-R1.subsampled.67.merged.bam",
+ "test_bam_to_pbam.se_bam" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/input/se/bams/rep1/rep1.subsampled.25.merged.bam",
 
- "test_bam_to_pbam.ref_pe_samtools_flagstat_qc" : "chip-seq-pipeline-test-data/ref_output/test_bam_to_pbam/pe/flagstat.qc",
- "test_bam_to_pbam.ref_se_samtools_flagstat_qc" : "chip-seq-pipeline-test-data/ref_output/test_bam_to_pbam/se/flagstat.qc"
+ "test_bam_to_pbam.ref_pe_samtools_flagstat_qc" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/ref_output/test_bam_to_pbam/pe/flagstat.qc",
+ "test_bam_to_pbam.ref_se_samtools_flagstat_qc" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/ref_output/test_bam_to_pbam/se/flagstat.qc"
 }

dev/test/test_task/test_bowtie2.json

@@ -1,20 +1,20 @@
 {
- "test_bowtie2.pe_bowtie2_idx_tar" : "chip-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" : "chip-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.pe_bowtie2_idx_tar" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-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-chip-seq-pipeline/chip-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.pe_fastqs_R1" : [
- "chip-seq-pipeline-test-data/input/pe/fastqs/rep1/pair1/rep1-R1.subsampled.67.fastq.gz"
+ "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/input/pe/fastqs/rep1/pair1/rep1-R1.subsampled.67.fastq.gz"
  ],
  "test_bowtie2.pe_fastqs_R2" : [
- "chip-seq-pipeline-test-data/input/pe/fastqs/rep1/pair2/rep1-R2.subsampled.67.fastq.gz"
+ "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/input/pe/fastqs/rep1/pair2/rep1-R2.subsampled.67.fastq.gz"
  ],
  "test_bowtie2.se_fastqs" : [
- "chip-seq-pipeline-test-data/input/se/fastqs/rep1/rep1.subsampled.25.fastq.gz"
+ "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/input/se/fastqs/rep1/rep1.subsampled.25.fastq.gz"
  ],
- "test_bowtie2.ref_pe_flagstat" : "chip-seq-pipeline-test-data/ref_output/test_bowtie2/pe/rep1-R1.subsampled.67.samstats.qc",
- "test_bowtie2.ref_se_flagstat" : "chip-seq-pipeline-test-data/ref_output/test_bowtie2/se/rep1.subsampled.25.samstats.qc",
+ "test_bowtie2.ref_pe_flagstat" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/ref_output/test_bowtie2/pe/rep1-R1.subsampled.67.samstats.qc",
+ "test_bowtie2.ref_se_flagstat" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/ref_output/test_bowtie2/se/rep1.subsampled.25.samstats.qc",
 
- "test_bowtie2.ref_pe_local_flagstat" : "chip-seq-pipeline-test-data/ref_output/test_bowtie2/pe/local/rep1-R1.subsampled.67.srt.samstats.qc",
- "test_bowtie2.ref_se_local_flagstat" : "chip-seq-pipeline-test-data/ref_output/test_bowtie2/se/local/rep1.subsampled.25.srt.samstats.qc"
+ "test_bowtie2.ref_pe_local_flagstat" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/ref_output/test_bowtie2/pe/local/rep1-R1.subsampled.67.srt.samstats.qc",
+ "test_bowtie2.ref_se_local_flagstat" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/ref_output/test_bowtie2/se/local/rep1.subsampled.25.srt.samstats.qc"
 
 }

dev/test/test_task/test_bwa.json

@@ -1,17 +1,17 @@
 {
- "test_bwa.pe_bwa_idx_tar" : "chip-seq-pipeline-test-data/genome_data/hg38_chr19_chrM/bwa_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta.tar",
- "test_bwa.se_bwa_idx_tar" : "chip-seq-pipeline-test-data/genome_data/hg38_chr19_chrM/bwa_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta.tar",
+ "test_bwa.pe_bwa_idx_tar" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/genome_data/hg38_chr19_chrM/bwa_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta.tar",
+ "test_bwa.se_bwa_idx_tar" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/genome_data/hg38_chr19_chrM/bwa_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta.tar",
 
  "test_bwa.pe_fastqs_R1" : [
- "chip-seq-pipeline-test-data/input/pe/fastqs/rep1/pair1/rep1-R1.subsampled.67.fastq.gz"
+ "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/input/pe/fastqs/rep1/pair1/rep1-R1.subsampled.67.fastq.gz"
  ],
  "test_bwa.pe_fastqs_R2" : [
- "chip-seq-pipeline-test-data/input/pe/fastqs/rep1/pair2/rep1-R2.subsampled.67.fastq.gz"
+ "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/input/pe/fastqs/rep1/pair2/rep1-R2.subsampled.67.fastq.gz"
  ],
  "test_bwa.se_fastqs" : [
- "chip-seq-pipeline-test-data/input/se/fastqs/rep1/rep1.subsampled.25.fastq.gz"
+ "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/input/se/fastqs/rep1/rep1.subsampled.25.fastq.gz"
  ],
 
- "test_bwa.ref_pe_flagstat" : "chip-seq-pipeline-test-data/ref_output/test_bwa/pe/rep1-R1.subsampled.67.samstats.qc",
- "test_bwa.ref_se_flagstat" : "chip-seq-pipeline-test-data/ref_output/test_bwa/se/rep1.subsampled.25.samstats.qc"
+ "test_bwa.ref_pe_flagstat" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/ref_output/test_bwa/pe/rep1-R1.subsampled.67.samstats.qc",
+ "test_bwa.ref_se_flagstat" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/ref_output/test_bwa/se/rep1.subsampled.25.samstats.qc"
 }

dev/test/test_task/test_choose_ctl.json

@@ -1,10 +1,10 @@
 {
- "test_choose_ctl.se_ta_rep1" : "chip-seq-pipeline-test-data/input/se/tas/rep1/rep1.subsampled.25.merged.nodup.tagAlign.gz",
- "test_choose_ctl.se_ta_rep2" : "chip-seq-pipeline-test-data/input/se/tas/rep2/rep2.subsampled.20.merged.nodup.tagAlign.gz",
- "test_choose_ctl.se_ta_pooled" : "chip-seq-pipeline-test-data/input/se/tas/pooled_rep/rep1.subsampled.25.merged.nodup.pooled.tagAlign.gz",
- "test_choose_ctl.se_ctl_ta_rep1" : "chip-seq-pipeline-test-data/input/se/tas/ctl1_fake_doubled/ctl1.double.tagAlign.gz",
- "test_choose_ctl.se_ctl_ta_rep2" : "chip-seq-pipeline-test-data/input/se/tas/ctl2_fake_doubled/ctl2.double.tagAlign.gz",
- "test_choose_ctl.se_ctl_ta_pooled" : "chip-seq-pipeline-test-data/input/se/tas/pooled_ctl_fake_doubled/ctl_pooled.double.tagnAlign.gz",
+ "test_choose_ctl.se_ta_rep1" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/input/se/tas/rep1/rep1.subsampled.25.merged.nodup.tagAlign.gz",
+ "test_choose_ctl.se_ta_rep2" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/input/se/tas/rep2/rep2.subsampled.20.merged.nodup.tagAlign.gz",
+ "test_choose_ctl.se_ta_pooled" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/input/se/tas/pooled_rep/rep1.subsampled.25.merged.nodup.pooled.tagAlign.gz",
+ "test_choose_ctl.se_ctl_ta_rep1" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/input/se/tas/ctl1_fake_doubled/ctl1.double.tagAlign.gz",
+ "test_choose_ctl.se_ctl_ta_rep2" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/input/se/tas/ctl2_fake_doubled/ctl2.double.tagAlign.gz",
+ "test_choose_ctl.se_ctl_ta_pooled" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/input/se/tas/pooled_ctl_fake_doubled/ctl_pooled.double.tagnAlign.gz",
 
  "test_choose_ctl.ref_se_choose_ctl_idx1" : 0,
  "test_choose_ctl.ref_se_choose_ctl_idx2" : 1,

dev/test/test_task/test_count_signal_track.json

@@ -1,8 +1,8 @@
 {
- "test_count_signal_track.se_chrsz" : "chip-seq-pipeline-test-data/genome_data/hg38_chr19_chrM/hg38_chr19_chrM.chrom.sizes",
+ "test_count_signal_track.se_chrsz" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/genome_data/hg38_chr19_chrM/hg38_chr19_chrM.chrom.sizes",
 
- "test_count_signal_track.se_ta" : "chip-seq-pipeline-test-data/input/se/tas/rep1/rep1.subsampled.25.merged.nodup.tagAlign.gz",
+ "test_count_signal_track.se_ta" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/input/se/tas/rep1/rep1.subsampled.25.merged.nodup.tagAlign.gz",
 
- "test_count_signal_track.ref_se_count_signal_track_pos_bw" : "chip-seq-pipeline-test-data/ref_output/test_count_signal_track/rep1.subsampled.25.merged.nodup.positive.bigwig",
- "test_count_signal_track.ref_se_count_signal_track_neg_bw" : "chip-seq-pipeline-test-data/ref_output/test_count_signal_track/rep1.subsampled.25.merged.nodup.negative.bigwig"
+ "test_count_signal_track.ref_se_count_signal_track_pos_bw" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/ref_output/test_count_signal_track/rep1.subsampled.25.merged.nodup.positive.bigwig",
+ "test_count_signal_track.ref_se_count_signal_track_neg_bw" : "gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data/ref_output/test_count_signal_track/rep1.subsampled.25.merged.nodup.negative.bigwig"
 }