output gff is now a separate history item (#34)

* output gff is now a separate histroy item

* changed tests back to expect failure

---------

Co-authored-by: Richard C. Burhans <[email protected]>

tools/ncbi_egapx/ncbi_egapx.xml

@@ -109,15 +109,27 @@
     </conditional>
     </inputs>
     <outputs>
-      <collection name="egapx_out" type="list" label="Outputs from egapx">
-        <discover_datasets pattern="__name_and_ext__" directory="egapx_out" visible="false"/>
+      <data name="output" format="gff" label="EGAPx annotation for ${on_string}" from_work_dir="egapx_out/accept.gff"/>
+      <collection name="nextflow_stats" label="EGAPx nextflow stats for ${on_string}" type="list">
+        <data name="nf_log" format="txt" label="Nextflow execution log" from_work_dir="egapx_out/nextflow.log"/>
+        <data name="nf_report" format="html" label="Nextflow execution report" from_work_dir="egapx_out/run.report.html"/>
+        <data name="nf_trace" format="tabular" label="Nextflow trace file" from_work_dir="egapx_out/run.trace.txt"/>
+        <data name="nf_timeline" format="html" label="Nextflow execution timeline" from_work_dir="egapx_out/run.timeline.html"/>
+        <data name="nf_params" format="yaml" label="Nextflow run parameters" from_work_dir="egapx_out/run_params.yaml"/>
       </collection>
     </outputs>
     <tests>
       <test expect_test_failure="true">
         <param name="input_style" value="history"/>
         <param name="yamlin" value="input.yaml"/>
-        <output_collection name="egapx_out" type="list" count="8"/>
+        <output name="output"><assert_contents><has_size min="1"/></assert_contents></output>
+        <output_collection name="nextflow_stats" type="list">
+          <element name="nf_log"><assert_contents><has_size min="1"/></assert_contents></element>
+          <element name="nf_report"><assert_contents><has_size min="1"/></assert_contents></element>
+          <element name="nf_trace"><assert_contents><has_size min="1"/></assert_contents></element>
+          <element name="nf_timeline"><assert_contents><has_size min="1"/></assert_contents></element>
+          <element name="nf_params"><assert_contents><has_size min="1"/></assert_contents></element>
+        </output_collection>
       </test>
       <test expect_test_failure="true">
         <param name="input_style" value="fillform"/>
@@ -127,7 +139,14 @@
         <param name="rna_type_select" value="list"/>
         <param name="rnaseq" value="https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572.1 https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572.2 https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248.1 https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248.2"/>
         <param name="xtra" value="proteins: []&#10;hmm: https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/gnomon/hmm_parameters/6956.params&#10;tasks:&#10;  star_wnode:&#10;    star_wnode: -cpus-per-worker 4"/>
-        <output_collection name="egapx_out" type="list" count="8"/>
+        <output name="output"><assert_contents><has_size min="1"/></assert_contents></output>
+        <output_collection name="nextflow_stats" type="list">
+          <element name="nf_log"><assert_contents><has_size min="1"/></assert_contents></element>
+          <element name="nf_report"><assert_contents><has_size min="1"/></assert_contents></element>
+          <element name="nf_trace"><assert_contents><has_size min="1"/></assert_contents></element>
+          <element name="nf_timeline"><assert_contents><has_size min="1"/></assert_contents></element>
+          <element name="nf_params"><assert_contents><has_size min="1"/></assert_contents></element>
+        </output_collection>
       </test>
     </tests>
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