Add conda environment names (#4327)

* feat: Add a first pass script * fix: Just use sed * refactor: Add name: field to every environment.yml
nf-core · Nov 14, 2023 · 3f5420a · 3f5420a
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diff --git a/.github/conda_env_names.bash b/.github/conda_env_names.bash
@@ -0,0 +1,12 @@
+#!/usr/bin/env cached-nix-shell
+#! nix-shell -p fd yq-go
+
+# Find all the environment.ymls
+ENV_FILES=$(fd "^environment.yml$" modules/)
+
+for file in $ENV_FILES; do
+    # Get the "name" field from the meta.yml next to the file
+    name=$(yq -r '.name' $(dirname "$file")/meta.yml)
+    # Add a name field in the enviroment.yml at the top of the file
+    sed -i "1s|^|name: $name\n|" "$file"
+done
diff --git a/modules/nf-core/abacas/environment.yml b/modules/nf-core/abacas/environment.yml
@@ -1,3 +1,4 @@
+name: abacas
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/abricate/run/environment.yml b/modules/nf-core/abricate/run/environment.yml
@@ -1,3 +1,4 @@
+name: abricate_run
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/abricate/summary/environment.yml b/modules/nf-core/abricate/summary/environment.yml
@@ -1,3 +1,4 @@
+name: abricate_summary
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/abritamr/run/environment.yml b/modules/nf-core/abritamr/run/environment.yml
@@ -1,3 +1,4 @@
+name: abritamr_run
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/adapterremoval/environment.yml b/modules/nf-core/adapterremoval/environment.yml
@@ -1,3 +1,4 @@
+name: adapterremoval
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/adapterremovalfixprefix/environment.yml b/modules/nf-core/adapterremovalfixprefix/environment.yml
@@ -1,3 +1,4 @@
+name: adapterremovalfixprefix
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/admixture/environment.yml b/modules/nf-core/admixture/environment.yml
@@ -1,3 +1,4 @@
+name: admixture
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/affy/justrma/environment.yml b/modules/nf-core/affy/justrma/environment.yml
@@ -1,3 +1,4 @@
+name: affy_justrma
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/agat/convertspgff2gtf/environment.yml b/modules/nf-core/agat/convertspgff2gtf/environment.yml
@@ -1,3 +1,4 @@
+name: agat_convertspgff2gtf
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/agat/convertspgff2tsv/environment.yml b/modules/nf-core/agat/convertspgff2tsv/environment.yml
@@ -1,3 +1,4 @@
+name: agat_convertspgff2tsv
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/agat/convertspgxf2gxf/environment.yml b/modules/nf-core/agat/convertspgxf2gxf/environment.yml
@@ -1,3 +1,4 @@
+name: agat_convertspgxf2gxf
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/agat/spstatistics/environment.yml b/modules/nf-core/agat/spstatistics/environment.yml
@@ -1,3 +1,4 @@
+name: agat_spstatistics
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/agat/sqstatbasic/environment.yml b/modules/nf-core/agat/sqstatbasic/environment.yml
@@ -1,3 +1,4 @@
+name: agat_sqstatbasic
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/agrvate/environment.yml b/modules/nf-core/agrvate/environment.yml
@@ -1,3 +1,4 @@
+name: agrvate
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/allelecounter/environment.yml b/modules/nf-core/allelecounter/environment.yml
@@ -1,3 +1,4 @@
+name: allelecounter
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/ampcombi/environment.yml b/modules/nf-core/ampcombi/environment.yml
@@ -1,3 +1,4 @@
+name: ampcombi
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/ampir/environment.yml b/modules/nf-core/ampir/environment.yml
@@ -1,3 +1,4 @@
+name: ampir
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/amplify/predict/environment.yml b/modules/nf-core/amplify/predict/environment.yml
@@ -1,3 +1,4 @@
+name: amplify_predict
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/amps/environment.yml b/modules/nf-core/amps/environment.yml
@@ -1,3 +1,4 @@
+name: amps
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/amrfinderplus/run/environment.yml b/modules/nf-core/amrfinderplus/run/environment.yml
@@ -1,3 +1,4 @@
+name: amrfinderplus_run
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/amrfinderplus/update/environment.yml b/modules/nf-core/amrfinderplus/update/environment.yml
@@ -1,3 +1,4 @@
+name: amrfinderplus_update
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/angsd/contamination/environment.yml b/modules/nf-core/angsd/contamination/environment.yml
@@ -1,3 +1,4 @@
+name: angsd_contamination
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/angsd/docounts/environment.yml b/modules/nf-core/angsd/docounts/environment.yml
@@ -1,3 +1,4 @@
+name: angsd_docounts
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/annotsv/annotsv/environment.yml b/modules/nf-core/annotsv/annotsv/environment.yml
@@ -1,3 +1,4 @@
+name: annotsv_annotsv
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/annotsv/installannotations/environment.yml b/modules/nf-core/annotsv/installannotations/environment.yml
@@ -1,3 +1,4 @@
+name: annotsv_installannotations
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/antismash/antismashlite/environment.yml b/modules/nf-core/antismash/antismashlite/environment.yml
@@ -1,3 +1,4 @@
+name: antismash_antismashlite
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/environment.yml b/modules/nf-core/antismash/antismashlitedownloaddatabases/environment.yml
@@ -1,3 +1,4 @@
+name: antismash_antismashlitedownloaddatabases
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/arcashla/extract/environment.yml b/modules/nf-core/arcashla/extract/environment.yml
@@ -1,3 +1,4 @@
+name: arcashla_extract
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/aria2/environment.yml b/modules/nf-core/aria2/environment.yml
@@ -1,3 +1,4 @@
+name: aria2
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/ariba/getref/environment.yml b/modules/nf-core/ariba/getref/environment.yml
@@ -1,3 +1,4 @@
+name: ariba_getref
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/ariba/run/environment.yml b/modules/nf-core/ariba/run/environment.yml
@@ -1,3 +1,4 @@
+name: ariba_run
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/arriba/arriba/environment.yml b/modules/nf-core/arriba/arriba/environment.yml
@@ -1,3 +1,4 @@
+name: arriba_arriba
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/arriba/download/environment.yml b/modules/nf-core/arriba/download/environment.yml
@@ -1,3 +1,4 @@
+name: arriba_download
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/art/illumina/environment.yml b/modules/nf-core/art/illumina/environment.yml
@@ -1,3 +1,4 @@
+name: art_illumina
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/artic/guppyplex/environment.yml b/modules/nf-core/artic/guppyplex/environment.yml
@@ -1,3 +1,4 @@
+name: artic_guppyplex
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/artic/minion/environment.yml b/modules/nf-core/artic/minion/environment.yml
@@ -1,3 +1,4 @@
+name: artic_minion
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/ascat/environment.yml b/modules/nf-core/ascat/environment.yml
@@ -1,3 +1,4 @@
+name: ascat
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/ashlar/environment.yml b/modules/nf-core/ashlar/environment.yml
@@ -1,3 +1,4 @@
+name: ashlar
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/assemblyscan/environment.yml b/modules/nf-core/assemblyscan/environment.yml
@@ -1,3 +1,4 @@
+name: assemblyscan
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/ataqv/ataqv/environment.yml b/modules/nf-core/ataqv/ataqv/environment.yml
@@ -1,3 +1,4 @@
+name: ataqv_ataqv
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/ataqv/mkarv/environment.yml b/modules/nf-core/ataqv/mkarv/environment.yml
@@ -1,3 +1,4 @@
+name: ataqv_mkarv
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/atlas/call/environment.yml b/modules/nf-core/atlas/call/environment.yml
@@ -1,3 +1,4 @@
+name: atlas_call
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/atlas/pmd/environment.yml b/modules/nf-core/atlas/pmd/environment.yml
@@ -1,3 +1,4 @@
+name: atlas_pmd
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/atlas/recal/environment.yml b/modules/nf-core/atlas/recal/environment.yml
@@ -1,3 +1,4 @@
+name: atlas_recal
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/atlas/splitmerge/environment.yml b/modules/nf-core/atlas/splitmerge/environment.yml
@@ -1,3 +1,4 @@
+name: atlas_splitmerge
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml
@@ -1,3 +1,4 @@
+name: atlasgeneannotationmanipulation_gtf2featureannotation
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/authentict/deam2cont/environment.yml b/modules/nf-core/authentict/deam2cont/environment.yml
@@ -1,3 +1,4 @@
+name: authentict_deam2cont
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/backsub/environment.yml b/modules/nf-core/backsub/environment.yml
@@ -1,3 +1,4 @@
+name: backsub
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bacphlip/environment.yml b/modules/nf-core/bacphlip/environment.yml
@@ -1,3 +1,4 @@
+name: bacphlip
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bakta/bakta/environment.yml b/modules/nf-core/bakta/bakta/environment.yml
@@ -1,3 +1,4 @@
+name: bakta_bakta
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bakta/baktadbdownload/environment.yml b/modules/nf-core/bakta/baktadbdownload/environment.yml
@@ -1,3 +1,4 @@
+name: bakta_baktadbdownload
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bamaligncleaner/environment.yml b/modules/nf-core/bamaligncleaner/environment.yml
@@ -1,3 +1,4 @@
+name: bamaligncleaner
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bamcmp/environment.yml b/modules/nf-core/bamcmp/environment.yml
@@ -1,3 +1,4 @@
+name: bamcmp
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bamtools/convert/environment.yml b/modules/nf-core/bamtools/convert/environment.yml
@@ -1,3 +1,4 @@
+name: bamtools_convert
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bamtools/split/environment.yml b/modules/nf-core/bamtools/split/environment.yml
@@ -1,3 +1,4 @@
+name: bamtools_split
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bamtools/stats/environment.yml b/modules/nf-core/bamtools/stats/environment.yml
@@ -1,3 +1,4 @@
+name: bamtools_stats
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bamutil/trimbam/environment.yml b/modules/nf-core/bamutil/trimbam/environment.yml
@@ -1,3 +1,4 @@
+name: bamutil_trimbam
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bandage/image/environment.yml b/modules/nf-core/bandage/image/environment.yml
@@ -1,3 +1,4 @@
+name: bandage_image
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/barrnap/environment.yml b/modules/nf-core/barrnap/environment.yml
@@ -1,3 +1,4 @@
+name: barrnap
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bases2fastq/environment.yml b/modules/nf-core/bases2fastq/environment.yml
@@ -1,3 +1,4 @@
+name: bases2fastq
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/basicpy/environment.yml b/modules/nf-core/basicpy/environment.yml
@@ -1,3 +1,4 @@
+name: basicpy
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bbmap/align/environment.yml b/modules/nf-core/bbmap/align/environment.yml
@@ -1,3 +1,4 @@
+name: bbmap_align
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bbmap/bbduk/environment.yml b/modules/nf-core/bbmap/bbduk/environment.yml
@@ -1,3 +1,4 @@
+name: bbmap_bbduk
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bbmap/bbnorm/environment.yml b/modules/nf-core/bbmap/bbnorm/environment.yml
@@ -1,3 +1,4 @@
+name: bbmap_bbnorm
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bbmap/bbsplit/environment.yml b/modules/nf-core/bbmap/bbsplit/environment.yml
@@ -1,3 +1,4 @@
+name: bbmap_bbsplit
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bbmap/clumpify/environment.yml b/modules/nf-core/bbmap/clumpify/environment.yml
@@ -1,3 +1,4 @@
+name: bbmap_clumpify
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bbmap/index/environment.yml b/modules/nf-core/bbmap/index/environment.yml
@@ -1,3 +1,4 @@
+name: bbmap_index
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bbmap/pileup/environment.yml b/modules/nf-core/bbmap/pileup/environment.yml
@@ -1,3 +1,4 @@
+name: bbmap_pileup
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bbmap/sendsketch/environment.yml b/modules/nf-core/bbmap/sendsketch/environment.yml
@@ -1,3 +1,4 @@
+name: bbmap_sendsketch
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bcftools/annotate/environment.yml b/modules/nf-core/bcftools/annotate/environment.yml
@@ -1,3 +1,4 @@
+name: bcftools_annotate
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bcftools/call/environment.yml b/modules/nf-core/bcftools/call/environment.yml
@@ -1,3 +1,4 @@
+name: bcftools_call
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bcftools/concat/environment.yml b/modules/nf-core/bcftools/concat/environment.yml
@@ -1,3 +1,4 @@
+name: bcftools_concat
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bcftools/consensus/environment.yml b/modules/nf-core/bcftools/consensus/environment.yml
@@ -1,3 +1,4 @@
+name: bcftools_consensus
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bcftools/convert/environment.yml b/modules/nf-core/bcftools/convert/environment.yml
@@ -1,3 +1,4 @@
+name: bcftools_convert
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bcftools/filter/environment.yml b/modules/nf-core/bcftools/filter/environment.yml
@@ -1,3 +1,4 @@
+name: bcftools_filter
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bcftools/index/environment.yml b/modules/nf-core/bcftools/index/environment.yml
@@ -1,3 +1,4 @@
+name: bcftools_index
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bcftools/isec/environment.yml b/modules/nf-core/bcftools/isec/environment.yml
@@ -1,3 +1,4 @@
+name: bcftools_isec
 channels:
   - conda-forge
   - bioconda