v2.2.2

Fixed broken docker cache and rebuilt docker image, and then synced with atac-seq-pipeline's image.

v2.2.1

• Fixed the issue that test run takes too much resources. Now users can run a test pipeline on a laptop.
• Fixed conflicts in Conda installer.
• Updated documentation:
  • Pipeline still supports Conda as an optional method, DACC will no longer help fixing Conda conflicts on user's computer. If any error occurs, then switch to Singularity method.
  • More comprehensive and simpler and README

v2.2.0

Upgrade Caper to >=2.2.0 for new HPC features.

$ pip install caper>=2.2.0 --upgrade

Conda environment name change:

• encode-chip-seq-pipeline -> encd-chip
• Please reinstall your Conda environment after updating pipeline's git repo.

  $ scripts/uninstall_conda_env.sh
  $ scripts/install_conda_env.sh

Caper's new HPC feature

• Unified command caper hpc for all HPC backend types (slurm, sge, pbs and lsf).
• Read Caper's README carefully and make a backup of your Caper's conf file (~/.caper/default.conf) and run caper init YOUR_BACKEND.
• caper hpc submit chip.wdl -i INPUT.json --leader-job-name GOOD_NAME_FOR_LEADER [--conda | --singularity]: submits a workflow to HPC's job engine.
• caper hpc list: shows all Caper leader jobs
• caper hpc abort JOB_ID: terminate a Caper leader job including child jobs

v2.1.6

Fixed python2 shebang

STDERR_BACKGROUND_CONTENTS=
Traceback (most recent call last):
  File "/home/zhaosj/anaconda3/envs/encode-atac-seq-pipeline/bin/encode_task_filter.py", line 438, in <module>
    main()
  File "/home/zhaosj/anaconda3/envs/encode-atac-seq-pipeline/bin/encode_task_filter.py", line 344, in main
    args.nth, args.mem_gb, args.out_dir)
  File "/home/zhaosj/anaconda3/envs/encode-atac-seq-pipeline/bin/encode_task_filter.py", line 136, in rm_unmapped_lowq_reads_pe
    res_param=get_samtools_res_param('fixmate', nth=nth),
  File "/home/zhaosj/anaconda3/envs/encode-atac-seq-pipeline/bin/encode_lib_common.py", line 359, in run_shell_cmd
    raise Exception(err_str)
Exception: PID=44241, PGID=44241, RC=127, DURATION_SEC=0.0
STDERR=/usr/bin/env: ‘python2’: No such file or directory

v2.1.5

• Fixed spp's nth parameter
• Fixed Conda dependency issues (readline, ncurses)

v2.1.4

• Fixed Conda libreadline.so.6 issue
• Show more info in final HTML report

Conda users need to update (or reinstall) pipeline's Conda environment.

$ scripts/update_conda_env.sh

v2.1.2

Hotfix for Conda environment error (missing package bedClip).

Conda users should re-install pipeline's Conda environments.

$ bash scripts/uninstall_conda_env.sh
$ bash scripts/install_conda_env.sh

v2.1.1

Hotfix for DNAnexus on dockstore

v2.1.0

Hotfix for chip.subsample_reads bug.

This bug was introduced in v1.2.2 (6/13/2019).
chip.ctl_subsample_reads is ignored and chip.subsample_reads (0: disabled by default) is used for subsampling both experiment replicates and controls.

Outputs are affected by this bug if chip.subsample_reads is non-zero and chip.pipeline_type is tf (default) or histone.
Since chip.subsample_reads is 0 (disabled) by default, outputs are not affected if you used a default set of parameters.

The following outputs can be affected by this bug:

• Control TAG-ALIGNs and all its downstream analyses.
• Such downstream outputs include all kinds of peaks (spp, macs2, idr, overlap).

v2.0.1

Fixed WDL for Dockstore (DNAnexus, Terra/Anvil) compatibility.
Updated documentation and metadata for Dockstore.