Merge pull request #7 from bio-raum/dev

Dev
bio-raum · Sep 10, 2024 · 2ef1f25 · 2ef1f25
2 parents cea8d49 + ab7ea4e
commit 2ef1f25
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Showing 11 changed files with 8 additions and 9 deletions.
diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@
 
 If you are really impatient, check out our [quickstart](docs/quickstart.md) guide. 
 
-![schema](images/GABI_Schema_v4.png)
+![schema](images/GABI_Schema_v5.png)
 
 ## Documentation 
 

diff --git a/docs/output.md b/docs/output.md
@@ -49,6 +49,8 @@ QUAST provides some insights into the assembly quality - with some caveats conce
 
 ![quast](../images/multiqc_quast.png)
 
+Also see our [troubleshooting](troubleshooting.md) document for more explanations on the limitation of Quast as used by GABI. 
+
 #### Busco
 
 BUSCO identifies the presence of expected conserved bacterial genes - a good assembly should be near-complete and not contain (many) duplicated BUSCOs. 

diff --git a/images/GABI_Schema_v4.png b/images/GABI_Schema_v4.png
diff --git a/images/GABI_Schema_v5.png b/images/GABI_Schema_v5.png
diff --git a/images/multiqc_busco.png b/images/multiqc_busco.png
diff --git a/images/multiqc_confindr.png b/images/multiqc_confindr.png
diff --git a/images/multiqc_general_stats.png b/images/multiqc_general_stats.png
diff --git a/images/multiqc_kraken.png b/images/multiqc_kraken.png
diff --git a/images/multiqc_quast.png b/images/multiqc_quast.png
diff --git a/lib/WorkflowPipeline.groovy b/lib/WorkflowPipeline.groovy
@@ -20,10 +20,7 @@ class WorkflowPipeline {
             log.info 'No --reference_base specified, cannot proceed!'
             System.exit(1)
         }
-        if (params.reference_fasta && !params.reference_gff || !params.reference_fasta && params.reference_gff) {
-            log.info 'You need to provide both a reference FASTA file and reference GFF file for Quast.'
-            System.exit(1)
-        }
+
     }
 
 }
diff --git a/workflows/gabi.nf b/workflows/gabi.nf
@@ -214,9 +214,9 @@ workflow GABI {
     */
     COVERAGE(
         ch_assemblies_clean,
-        ch_short_reads_only,
-        ch_ont_reads_only,
-        ch_pb_reads_only
+        ch_illumina_trimmed,
+        ch_ont_trimmed,
+        ch_pacbio_trimmed
     )
     ch_versions   = ch_versions.mix(COVERAGE.out.versions)
     ch_multiqc_illumina = ch_multiqc_illumina.mix(
@@ -372,7 +372,7 @@ workflow GABI {
         REPORT(
             ch_reports_grouped
         )
-        }
+    }
 
     /*
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~