Make prettier happy

nf-core · Jan 30, 2024 · 940b5b7 · 940b5b7
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Showing 5 changed files with 26 additions and 26 deletions.
diff --git a/docs/usage.md b/docs/usage.md
@@ -41,27 +41,27 @@ The typical commands for running the pipeline on AlphaFold2, Colabfold and ESMFo
 
 ```csv title="samplesheet.csv"
 nextflow run nf-core/proteinfold \
-       --input samplesheet.csv \
-       --outdir <OUTDIR> \
-       --mode alphafold2 \
-       --alphafold2_db <null (default) | DB_PATH> \
-       --full_dbs <true/false> \
-       --alphafold2_model_preset monomer \
-       --use_gpu <true/false> \
-       -profile <docker>
+      --input samplesheet.csv \
+      --outdir <OUTDIR> \
+      --mode alphafold2 \
+      --alphafold2_db <null (default) | DB_PATH> \
+      --full_dbs <true/false> \
+      --alphafold2_model_preset monomer \
+      --use_gpu <true/false> \
+      -profile <docker>
 ```
 
 ```console
 nextflow run nf-core/proteinfold \
-    --input samplesheet.csv \
-    --outdir <OUTDIR> \
-    --mode alphafold2 \
-    --alphafold2_mode split_msa_prediction \
-    --alphafold2_db <null (default) | DB_PATH> \
-    --full_dbs <true/false> \
-    --alphafold2_model_preset monomer \
-    --use_gpu <true/false> \
-    -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
+      --input samplesheet.csv \
+      --outdir <OUTDIR> \
+      --mode alphafold2 \
+      --alphafold2_mode split_msa_prediction \
+      --alphafold2_db <null (default) | DB_PATH> \
+      --full_dbs <true/false> \
+      --alphafold2_model_preset monomer \
+      --use_gpu <true/false> \
+      -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
 ```
 
 If you specify the `--alphafold2_db ` parameter, the directory structure of your path should be like this:
@@ -233,7 +233,7 @@ nextflow run nf-core/proteinfold \
       --colabfold_model_preset "AlphaFold2-ptm" \
       --use_gpu <true/false> \
       --db_load_mode 0
-       -profile <docker>
+      -profile <docker>
 ```
 
 ```console
@@ -248,7 +248,7 @@ nextflow run nf-core/proteinfold \
       --use_amber <true/false> \
       --colabfold_model_preset "AlphaFold2-ptm" \
       --use_gpu <true/false> \
-       -profile <docker>
+      -profile <docker>
 ```
 
 If you specify the `--colabfold_db ` parameter, the directory structure of your path should be like this:
@@ -395,7 +395,7 @@ nextflow run nf-core/proteinfold \
       --num_recycles 4 \
       --esmfold_model_preset <monomer/multimer> \
       --use_gpu <true/false> \
-       -profile <docker>
+      -profile <docker>
 ```
 
 If you specify the `--esmfold_db ` parameter, the directory structure of your path should be like this:

diff --git a/nextflow.config b/nextflow.config
@@ -168,8 +168,8 @@ profiles {
     docker {
         docker.enabled         = true
         docker.userEmulation   = true
-        if (params.use_gpu) { 
-            docker.runOptions = '--gpus all' 
+        if (params.use_gpu) {
+            docker.runOptions = '--gpus all'
         } else {
             docker.runOptions      = '-u $(id -u):$(id -g)'
         }

diff --git a/subworkflows/local/prepare_alphafold2_dbs.nf b/subworkflows/local/prepare_alphafold2_dbs.nf
@@ -120,7 +120,7 @@ workflow PREPARE_ALPHAFOLD2_DBS {
         ch_version =  ch_versions.mix(COMBINE_UNIPROT.out.versions)
     }
 
-	emit:
+    emit:
     bfd        = ch_bfd
     small_bfd  = ch_small_bfd
     params     = ch_params

diff --git a/subworkflows/local/prepare_colabfold_dbs.nf b/subworkflows/local/prepare_colabfold_dbs.nf
@@ -11,7 +11,7 @@ include { MMSEQS_TSV2EXPROFILEDB as MMSEQS_TSV2EXPROFILEDB_COLABFOLDDB } from '.
 include { MMSEQS_TSV2EXPROFILEDB as MMSEQS_TSV2EXPROFILEDB_UNIPROT30   } from '../../modules/nf-core/mmseqs/tsv2exprofiledb/main'
 
 workflow PREPARE_COLABFOLD_DBS {
-	main:
+    main:
     ch_params       = Channel.empty()
     ch_colabfold_db = Channel.empty()
     ch_uniref30     = Channel.empty()
@@ -72,7 +72,7 @@ workflow PREPARE_COLABFOLD_DBS {
         }
     }
 
-	emit:
+    emit:
     params       = ch_params
     colabfold_db = ch_colabfold_db
     uniref30     = ch_uniref30

diff --git a/workflows/colabfold.nf b/workflows/colabfold.nf
@@ -150,7 +150,7 @@ workflow COLABFOLD {
         ch_versions = ch_versions.mix(COLABFOLD_BATCH.out.versions)
     }
 
-     //
+    //
     // MODULE: Pipeline reporting
     //
     CUSTOM_DUMPSOFTWAREVERSIONS (
-Original file line number
+Diff line change
@@ Expand Up / @@ -150,7 +150,7 @@ workflow COLABFOLD { @@
             ch_versions = ch_versions.mix(COLABFOLD_BATCH.out.versions)
         }
-         //
+        //
         // MODULE: Pipeline reporting
         //
         CUSTOM_DUMPSOFTWAREVERSIONS (
@@ Expand Down @@