v2.2.3

Added troubleshooting/warning/instruction for PE Fastqs downloaded from SRA (paired read name issue). See README.md for details.

Fixed broken docker cache and rebuilt new image.

v2.2.2

Fixed zero length read after TN5 shifting.

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-atac-seq-pipeline -> encd-atac
• 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 atac.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

v2.1.3

Fixed python2 shebang (issue #359)

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

v2.1.2

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

v2.1.1

• 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

v2.1.0

Updated the default genome TSV file (v3 to v4) in test example input JSON.

• https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ_subsampled.json

The only difference between two genome TSV versions (v3 and v4) is in a reference TSS bed file.
Such TSS file's genome coordinate is shifted by 1 to be based on a zero-based index (the old TSS file was wrongly based on a one-based index).

Therefore, using a v4 genome TSV will slightly affect the output of the tss_enrich analysis.

v2.0.3

Hotfix for Conda environment error (missing package bedClip).

Conda users should re-install pipeline Conda environment.

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

v2.0.2

Hotfix for DNAnexsus on Dockstore