Merge pull request #48 from ENCODE-DCC/PIP-468_v1.1.6

Pip 468 v1.1.6

.circleci/config.yml

@@ -51,7 +51,7 @@ jobs:
           name: build image
           command: |
             source ${BASH_ENV}
-            export DOCKER_CACHE_TAG=v1.1.5
+            export DOCKER_CACHE_TAG=v1.1.6
             echo "pulling ${DOCKER_CACHE_TAG}!"
             docker pull quay.io/encode-dcc/chip-seq-pipeline:${DOCKER_CACHE_TAG}
             docker login -u=${QUAY_ROBOT_USER} -p=${QUAY_ROBOT_USER_TOKEN} quay.io

README.md

@@ -9,6 +9,7 @@ This ChIP-Seq pipeline is based off the ENCODE (phase-3) transcription factor an
 
 * **Flexibility**: Support for `docker`, `singularity` and `Conda`.
 * **Portability**: Support for many cloud platforms (Google/DNAnexus) and cluster engines (SLURM/SGE/PBS).
+* **Resumability**: [Resume](utils/qc_jsons_to_tsv/README.md) a failed workflow from where it left off.
 * **User-friendly HTML report**: tabulated quality metrics including alignment/peak statistics and FRiP along with many useful plots (IDR/cross-correlation measures).
   - Examples: [HTML](https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR000DYI/example_output/qc.html), [JSON](docs/example_output/v1.1.5/qc.json)
 * **Genomes**: Pre-built database for GRCh38, hg19, mm10, mm9 and additional support for custom genomes.
@@ -49,3 +50,11 @@ There are some useful tools to post-process outputs of the pipeline.
 ### qc_jsons_to_tsv
 
 [This tool](utils/qc_jsons_to_tsv/README.md) recursively finds and parses all `qc.json` (pipeline's [final output](docs/example_output/v1.1.5/qc.json)) found from a specified root directory. It generates a TSV file that has all quality metrics tabulated in rows for each experiment and replicate. This tool also estimates overall quality of a sample by [a criteria definition JSON file](utils/qc_jsons_to_tsv/criteria.default.json) which can be a good guideline for QC'ing experiments.
+
+### resumer
+
+[This tool](utils/resumer/README.md) parses a metadata JSON file from a previous failed workflow and generates a new input JSON file to start a pipeline from where it left off.
+
+### ENCODE downloader
+
+[This tool](https://github.com/kundajelab/ENCODE_downloader) downloads any type (FASTQ, BAM, PEAK, ...) of data from the ENCODE portal. It also generates a metadata JSON file per experiment which will be very useful to make an input JSON file for the pipeline.