Updated PFR params

Plant-Food-Research-Open · Apr 30, 2024 · eba68eb · eba68eb
1 parent 4355771
commit eba68eb
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Showing 4 changed files with 11 additions and 20 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -43,7 +43,7 @@ process {
 if(!params.skip_fastqc) {
     process {
         withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_RAW' {
-        ext.args   = '--quiet'
+            ext.args   = '--quiet'
         }
 
         withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_TRIM' {

diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
@@ -38,7 +38,6 @@ process FASTQC {
     fastqc \\
         $args \\
         --threads $task.cpus \\
-        --memory $fastqc_memory \\
         $renamed_files
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/pfr/params.json b/pfr/params.json
@@ -1,16 +1,8 @@
 {
-    "external_protein_fastas": [
-        "/workspace/ComparativeDataSources/OrthoDB11/Viridiplantae.fa.gz",
-        "/output/genomic/fairGenomes/Plant/Actinidia/chinensis/var_chinensis/male/2x/assembly_russell/v2.1/RU01.20221115150135.pep.fasta"
-    ],
-    "liftoff": [
-        [
-            "/output/genomic/fairGenomes/Plant/Actinidia/chinensis/var_chinensis/male/2x/assembly_russell/v2.1/Russell_V2a.chromosomes.and.unassiged.and.haplotigs.fsa",
-            "/output/genomic/fairGenomes/Plant/Actinidia/chinensis/var_chinensis/male/2x/assembly_russell/v2.1/RU01.20221115150135.gff3"
-        ],
-        [
-            "/output/genomic/fairGenomes/Plant/Arabidopsis/thaliana/var_na/sex_na/2x/assembly_tair/v10/TAIR10_chr_all.fas",
-            "/output/genomic/fairGenomes/Plant/Arabidopsis/thaliana/var_na/sex_na/2x/assembly_tair/v10/TAIR10_GFF3_genes_transposons.fixed.gff3"
-        ]
-    ]
+    "input": "/workspace/pangene/test_data/assemblysheet.csv",
+    "external_protein_fastas": "/workspace/pangene/test_data/external-protein-fastas.txt",
+    "eggnogmapper_db_dir": "/workspace/ComparativeDataSources/emapperdb/5.0.2",
+    "eggnogmapper_tax_scope": 33090,
+    "fastq": "/workspace/pangene/test_data/fastqsheet.csv",
+    "liftoff_annotations": "/workspace/pangene/test_data/liftoffannotations.csv"
 }
diff --git a/pfr/profile.config b/pfr/profile.config
@@ -11,7 +11,7 @@ profiles {
     }
 }
 
-params {
-    config_profile_name         = 'Plant&Food profile'
-    config_profile_description  = 'Plant&Food profile using SLURM in combination with Apptainer'
-}
+// params {
+//     config_profile_name         = 'Plant&Food profile'
+//     config_profile_description  = 'Plant&Food profile using SLURM in combination with Apptainer'
+// }