Merge pull request #563 from 4dn-dcic/add_atac_key

Add ATAC-seq file key to attr_keys

CHANGELOG.rst

@@ -7,6 +7,12 @@ foursight
 Change Log
 ----------
 
+4.4.2
+=====
+* Added 'input_bed' to attr_keys in wfr_utils.py's start_missing_run for ATAC-seq pipeline
+
+`PR 563: Add ATAC-seq file key to attr_keys <https://github.com/4dn-dcic/foursight/pull/563>`_
+
 4.4.1
 =====
 * updated check_setup to autoqueue chipseq check on data/prod

chalicelib_fourfront/checks/helpers/wfr_utils.py

@@ -1552,7 +1552,7 @@ def run_missing_wfr(input_json, input_files_and_params, run_name, auth, env, fs_
 def start_missing_run(run_info, auth, env, fs_env):
     attr_keys = ['fastq1', 'fastq', 'input_pairs', 'input_bams', 'input_fastqs',
                  'fastq_R1', 'input_bam', 'rna.fastqs_R1', 'mad_qc.quantfiles', 'mcoolfile',
-                 'chip.ctl_fastqs', 'chip.fastqs', 'chip.tas', 'atac.fastqs', 'atac.tas']
+                 'chip.ctl_fastqs', 'chip.fastqs', 'chip.tas', 'atac.fastqs', 'atac.tas', 'input_bed']
     run_settings = run_info[1]
     inputs = run_info[2]
     name_tag = run_info[3]
@@ -1577,7 +1577,7 @@ def start_missing_run(run_info, auth, env, fs_env):
     if not attr_file:
         possible_keys = [i for i in inputs.keys() if i != 'additional_file_parameters']
         error_message = ('one of these argument names {} which carry the input file -not the references-'
-                         ' should be added to att_keys dictionary on foursight cgap_utils.py function start_missing_run').format(possible_keys)
+                         ' should be added to att_keys dictionary on foursight cgap_utils.py or attr_keys in wfr_utils.py function start_missing_run').format(possible_keys)
         raise ValueError(error_message)
     attributions = get_attribution(ff_utils.get_metadata(attr_file, auth))
     settings = wfrset_utils.step_settings(run_settings[0], run_settings[1], attributions, run_settings[2])

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "foursight"
-version = "4.4.1"
+version = "4.4.2"
 description = "Serverless Chalice Application for Monitoring"
 authors = ["4DN-DCIC Team <[email protected]>"]
 license = "MIT"