Merge pull request #31 from ENCODE-DCC/PIP-711_prerelease_chores

Pip 711 prerelease chores
ENCODE-DCC · Aug 26, 2019 · 8ee6a0f · 8ee6a0f
2 parents 246f325 + 1eb6021
commit 8ee6a0f
Show file tree

Hide file tree

Showing 6 changed files with 11 additions and 9 deletions.
diff --git a/docs/reference.md b/docs/reference.md
@@ -77,10 +77,10 @@ A typical `input.json` is structured in the following way:
 The following elaborates on the meaning of each line in the input file.
 
 * `long_read_rna_pipeline.fastqs` Is a list of gzipped input fastqs, one file per replicate.
-* `long_read_rna_pipeline.reference_genome` Is the gzipped fasta file containing the reference genome used in mapping.
-* `long_read_rna_pipeline.annotation` Is the gzipped gtf file containing the annotations.
-* `long_read_rna_pipeline.variants` Is the gzipped vcf file containing variants.
-* `long_read_rna_pipeline.splice_junctions` Is the splice junctions file, generated with `get-splice-junctions.wdl` workflow based on the annotation and reference genome. This will be made available for download from The ENCODE Portal.
+* `long_read_rna_pipeline.reference_genome` Is the gzipped fasta file containing the reference genome used in mapping. Files for [human](https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15/) and [mouse](https://www.encodeproject.org/files/mm10_no_alt_analysis_set_ENCODE/) are available on the [ENCODE Portal](https://https://www.encodeproject.org/).
+* `long_read_rna_pipeline.annotation` Is the gzipped gtf file containing the annotations. Files for [human V29](https://www.encodeproject.org/files/gencode.v29.primary_assembly.annotation_UCSC_names/) and [mouse M21](https://www.encodeproject.org/files/gencode.vM21.primary_assembly.annotation_UCSC_names/) are available on the [ENCODE Portal](https://https://www.encodeproject.org/).
+* `long_read_rna_pipeline.variants` Is the gzipped vcf file containing variants. File for [human](https://www.encodeproject.org/files/dbsnp-variants-00-common_all/) available on the [ENCODE Portal](https://https://www.encodeproject.org/). Not used for mouse, this input is optional and can be left undefined.
+* `long_read_rna_pipeline.splice_junctions` Is the splice junctions file, generated with `get-splice-junctions.wdl` workflow based on the annotation and reference genome. Files for [human](https://www.encodeproject.org/files/ENCFF055LPJ/) and [mouse](https://www.encodeproject.org/files/ENCFF495CGH/) are available on the [ENCODE Portal](https://https://www.encodeproject.org/).
 * `long_read_rna_pipeline.experiment_prefix` This will be a prefix for the output files.
 * `long_read_rna_pipeline.input_type` Platform that was used for generating the data. Options are `pacbio` and `nanopore`.
 * `long_read_rna_pipeline.genome_build` Genome build name in the initial TALON database. This is internal metadata variable you typically do not need to touch.

diff --git a/get-splice-junctions.wdl b/get-splice-junctions.wdl
@@ -1,6 +1,9 @@
 # ENCODE long read rna pipeline: get splice junctions
 # Maintainer: Otto Jolanki
 
+#CAPER docker quay.io/encode-dcc/long-read-rna-pipeline:v1.1
+#CAPER singularity docker://quay.io/encode-dcc/long-read-rna-pipeline:v1.1
+
 workflow get_splice_junctions {
     # Inputs
 

diff --git a/long-read-rna-pipeline.wdl b/long-read-rna-pipeline.wdl
@@ -1,8 +1,8 @@
 # ENCODE long read rna pipeline
 # Maintainer: Otto Jolanki
 
-#CAPER docker quay.io/encode-dcc/long-read-rna-pipeline:v1.0
-#CAPER singularity docker://quay.io/encode-dcc/long-read-rna-pipeline:v1.0
+#CAPER docker quay.io/encode-dcc/long-read-rna-pipeline:v1.1
+#CAPER singularity docker://quay.io/encode-dcc/long-read-rna-pipeline:v1.1
 
 workflow long_read_rna_pipeline {
     # Inputs

diff --git a/src/compare_md5.py b/src/compare_md5.py
@@ -4,7 +4,6 @@
 """
 
 __author__ = "Otto Jolanki"
-__version__ = "0.1.0"
 __license__ = "MIT"
 
 import argparse

diff --git a/workflow_opts/docker.json b/workflow_opts/docker.json
@@ -1,6 +1,6 @@
 {
     "default_runtime_attributes" : {
-        "docker" : "quay.io/encode-dcc/long-read-rna-pipeline:v1.0",
+        "docker" : "quay.io/encode-dcc/long-read-rna-pipeline:v1.1",
         "zones": "us-west1-a us-west1-b us-west1-c us-central1-c us-central1-b",
         "failOnStderr" : false,
         "continueOnReturnCode" : 0,

diff --git a/workflow_opts/singularity.json b/workflow_opts/singularity.json
@@ -1,6 +1,6 @@
 {
     "default_runtime_attributes" : {
-        "singularity_container" : "~/.singularity/long-read-rna-pipeline-v1.0.simg",
+        "singularity_container" : "~/.singularity/long-read-rna-pipeline-v1.1.simg",
         "singularity_bindpath" : "~/"
     }
 }