Merge branch 'main' into update-egapx

richard-burhans · Nov 15, 2024 · 0dfb5f1 · 0dfb5f1
2 parents e4bf7ac + a297eba
commit 0dfb5f1
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diff --git a/tools/ncbi_egapx/ncbi_egapx.xml b/tools/ncbi_egapx/ncbi_egapx.xml
@@ -81,7 +81,8 @@ $row
                         <param name="uri" type="text" label="URI pointing to the reference genome FASTA file"/>
                     </when>
                 </conditional>
-                <param name="taxid" type="integer" min="0" label="NCBI Taxon ID" help="Used to identify the HMM model files needed"/>
+                <param name="taxid" type="integer" min="0" value="0" label="NCBI Taxon ID" help="Used to identify the HMM model files needed"/>
+
                 <conditional name="condrnaseq">
                     <param name="rna_type_select" type="select" label="RNA sequence data source"
                         help="Select RNAseq input data from history or input a list of SRA identifiers or remote URI">

diff --git a/tools/ncbi_egapx/test-data/input.yaml b/tools/ncbi_egapx/test-data/input.yaml
@@ -3,15 +3,13 @@
 # To limit the requirements you also need to use -e docker_minimal
 
 genome: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/020/809/275/GCF_020809275.1_ASM2080927v1/GCF_020809275.1_ASM2080927v1_genomic.fna.gz
+taxid: 6954
 reads:
   - 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
-taxid: 6954
-proteins: []
 hmm: https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/gnomon/hmm_parameters/6956.params
 tasks:
   star_wnode:
     star_wnode: -cpus-per-worker 4
-