some fixes

qiita_db/metadata_template/prep_template.py

@@ -851,20 +851,30 @@ def _get_predecessors(workflow, node):
             starting_job = None
             pt_artifact = self.artifact.artifact_type
 
-        workflows = []
+        all_workflows = [wk for wk in qdb.software.DefaultWorkflow.iter()]
+        # are there any workflows with parameters?
+        check_requirements = False
+        default_parameters = {'prep': {}, 'sample': {}}
+        if [wk for wk in all_workflows if wk.parameters != default_parameters]:
+            check_requirements = True
         ST = qdb.metadata_template.sample_template.SampleTemplate
-        for wk in qdb.software.DefaultWorkflow.iter():
+        workflows = []
+        for wk in all_workflows:
             if wk.artifact_type == pt_artifact and pt_dt in wk.data_type:
+                if check_requirements and wk.parameters == default_parameters:
+                    continue
                 wk_params = wk.parameters
                 reqs_satisfied = True
 
                 if wk_params['sample']:
+                    check_requirements = True
                     df = ST(self.study_id).to_dataframe(samples=list(self))
                     for k, v in wk_params['sample'].items():
                         if k not in df.columns or v not in df[k].unique():
                             reqs_satisfied = False
 
                 if wk_params['prep']:
+                    check_requirements = True
                     df = self.to_dataframe()
                     for k, v in wk_params['prep'].items():
                         if k not in df.columns or v not in df[k].unique():

qiita_db/processing_job.py

@@ -999,7 +999,9 @@ def submit(self, parent_job_id=None, dependent_jobs_list=None):
             qdb.sql_connection.TRN.commit()
 
         job_dir = join(qdb.util.get_work_base_dir(), self.id)
-        software = self.command.software
+        command = self.command
+        software = command.software
+        cname = command.name
         plugin_start_script = software.start_script
         plugin_env_script = software.environment_script
 
@@ -1011,7 +1013,15 @@ def submit(self, parent_job_id=None, dependent_jobs_list=None):
         # case where we are going to execute some command and then wait for the
         # plugin to return their own id (first implemented for
         # fast-bowtie2+woltka)
-        if 'ENVIRONMENT' in plugin_env_script:
+        #
+        # This is the hardcoded lines described in issue:
+        # https://github.com/qiita-spots/qiita/issues/3340
+        # the idea is that in the future we shouldn't check specific command
+        # names to know if it should be executed differently and the
+        # plugin should let Qiita know that a specific command should be ran
+        # as job array or not
+        cnames_to_skip = {'Calculate Cell Counts'}
+        if 'ENVIRONMENT' in plugin_env_script and not cname in cnames_to_skip:
             # the job has to be in running state so the plugin can change its`
             # status
             with qdb.sql_connection.TRN:

qiita_pet/templates/workflows.html

@@ -73,9 +73,9 @@ <h3>Recommended Default Workflows</h3>
         default Earth Microbiome Project protocol and so assumes the uploaded data are multiplexed sequences with the reversed barcodes in your mapping file and index sequence
         file (<a href="https://earthmicrobiome.org/protocols-and-standards/" target="_blank">see here</a> for more details). Thus, if the protocol does not apply to your data
         you can still use the Default Workflow, however, you should first manually process your data using the appropriate steps until you have a defined step; in our example,
-        demultiplexed your reads. After demultiplexing the Default Workflow is safe to use with any protocol.
+        demultiplex your reads. After demultiplexing, the Default Workflow is safe to use with any protocol.
         <br/><br/>
-        If you have already manually performed one of the processing steps in the Defaul Workflow pipeline, the "Add Default Workflow" button will not re-select those steps but
+        If you have already manually performed one of the processing steps in the Default Workflow pipeline, the "Add Default Workflow" button will not re-select those steps but
         instead will only select any remaining steps that have not been completed. You can also add additional workflows on top of the recommended Default Workflow at any time.
         <br/><br/>
         Note that this is not a full inclusive list of data types accepted by Qiita but only those that have a defined workflow.