v1.3.6

Conda users should re-install pipeline's environment.

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

DNAnexus web-interface users should use workflows suffixed with -dockerhub. i.e. v1.3.6-dockerhub.

• New parameters (in an input JSON)
  • chip.crop_length: Crop FASTQs with Trimmomatic. Cropping is disabled by default (set as 0). Check your FASTQs' read length first. Any reads SHORTER than this length will be excluded while cropping, hence not included in output BAMs and all downstream analyses.
  • chip.fdr_thresh: FDR threshold for SPP peak caller. It's 0.01 by default. Use a more relaxed value if you see the following File is empty error in SPP task call-peak. Possible fix for issue #119.

	Traceback (most recent call last):
	  File "/root/miniconda3/envs/encode-chip-seq-pipeline/bin/encode_task_spp.py", line 103, in <module>
	    main()
	  File "/root/miniconda3/envs/encode-chip-seq-pipeline/bin/encode_task_spp.py", line 94, in main
	    assert_file_not_empty(rpeak)
	  File "/root/miniconda3/envs/encode-chip-seq-pipeline/bin/encode_lib_common.py", line 212, in assert_file_not_empty
	    raise Exception('File is empty ({}). Help: {}'.format(f, help))
	Exception: File is empty (rep2-R1.subsampled.50.merged.nodup.pr2_x_ctl_for_rep2.300K.regionPeak.gz). Help:

• Changes in parameters

  • chip.xcor_pe_trim_bp -> chip.xcor_trim_bp: _pe_ is misleading since it's also applied to SE FASTQs too.

• Bug fixes

  • Ungzipped single FASTQ input
  • DNAnexus: Failure at read_genome_tsv due to errors while retrieving image from quay.io. dockerhub is used instead.