From ca9d582a1410214322eca47096e3796dbde37b3b Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Thu, 24 Oct 2024 14:29:49 +0100 Subject: [PATCH] Removed references to "defaults" --- lib/Utils.groovy | 2 +- modules/nf-core/blast/blastn/environment.yml | 1 - modules/nf-core/busco/environment.yml | 1 - modules/nf-core/cat/cat/environment.yml | 1 - modules/nf-core/custom/dumpsoftwareversions/environment.yml | 1 - modules/nf-core/diamond/blastp/environment.yml | 1 - modules/nf-core/diamond/blastx/environment.yml | 1 - modules/nf-core/fastawindows/environment.yml | 1 - modules/nf-core/gunzip/environment.yml | 1 - modules/nf-core/minimap2/align/environment.yml | 1 - modules/nf-core/multiqc/environment.yml | 1 - modules/nf-core/pigz/compress/environment.yml | 1 - modules/nf-core/samtools/flagstat/environment.yml | 1 - modules/nf-core/samtools/index/environment.yml | 1 - modules/nf-core/samtools/view/environment.yml | 1 - modules/nf-core/seqtk/subseq/environment.yml | 1 - modules/nf-core/windowmasker/mkcounts/environment.yml | 1 - modules/nf-core/windowmasker/ustat/environment.yml | 1 - 18 files changed, 1 insertion(+), 18 deletions(-) diff --git a/lib/Utils.groovy b/lib/Utils.groovy index 8d030f4e..13cb02df 100755 --- a/lib/Utils.groovy +++ b/lib/Utils.groovy @@ -22,7 +22,7 @@ class Utils { // Check that all channels are present // This channel list is ordered by required channel priority. - def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] + def required_channels_in_order = ['conda-forge', 'bioconda'] def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order diff --git a/modules/nf-core/blast/blastn/environment.yml b/modules/nf-core/blast/blastn/environment.yml index cb9b15dd..7b73f6e5 100644 --- a/modules/nf-core/blast/blastn/environment.yml +++ b/modules/nf-core/blast/blastn/environment.yml @@ -2,6 +2,5 @@ name: blast_blastn channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::blast=2.14.1 diff --git a/modules/nf-core/busco/environment.yml b/modules/nf-core/busco/environment.yml index f872d057..dd7949a5 100644 --- a/modules/nf-core/busco/environment.yml +++ b/modules/nf-core/busco/environment.yml @@ -2,6 +2,5 @@ name: busco channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::busco=5.5.0 diff --git a/modules/nf-core/cat/cat/environment.yml b/modules/nf-core/cat/cat/environment.yml index 17a04ef2..a095841a 100644 --- a/modules/nf-core/cat/cat/environment.yml +++ b/modules/nf-core/cat/cat/environment.yml @@ -2,6 +2,5 @@ name: cat_cat channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::pigz=2.3.4 diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml index b48ced26..43f4828f 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/environment.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -2,6 +2,5 @@ name: custom_dumpsoftwareversions channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::multiqc=1.20 diff --git a/modules/nf-core/diamond/blastp/environment.yml b/modules/nf-core/diamond/blastp/environment.yml index 922ea7ed..95978dff 100644 --- a/modules/nf-core/diamond/blastp/environment.yml +++ b/modules/nf-core/diamond/blastp/environment.yml @@ -2,6 +2,5 @@ name: diamond_blastp channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::diamond=2.1.8 diff --git a/modules/nf-core/diamond/blastx/environment.yml b/modules/nf-core/diamond/blastx/environment.yml index 70d6857d..57f8abce 100644 --- a/modules/nf-core/diamond/blastx/environment.yml +++ b/modules/nf-core/diamond/blastx/environment.yml @@ -2,6 +2,5 @@ name: diamond_blastx channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::diamond=2.1.8 diff --git a/modules/nf-core/fastawindows/environment.yml b/modules/nf-core/fastawindows/environment.yml index ce557158..ab7bc227 100644 --- a/modules/nf-core/fastawindows/environment.yml +++ b/modules/nf-core/fastawindows/environment.yml @@ -2,6 +2,5 @@ name: fastawindows channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fasta_windows=0.2.4 diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml index 25910b34..5ac9b57b 100644 --- a/modules/nf-core/gunzip/environment.yml +++ b/modules/nf-core/gunzip/environment.yml @@ -2,6 +2,5 @@ name: gunzip channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::sed=4.7 diff --git a/modules/nf-core/minimap2/align/environment.yml b/modules/nf-core/minimap2/align/environment.yml index cf6e775f..42636729 100644 --- a/modules/nf-core/minimap2/align/environment.yml +++ b/modules/nf-core/minimap2/align/environment.yml @@ -2,7 +2,6 @@ name: minimap2_align channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::minimap2=2.24 - bioconda::samtools=1.18 diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index ca39fb67..329ddb48 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -2,6 +2,5 @@ name: multiqc channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::multiqc=1.21 diff --git a/modules/nf-core/pigz/compress/environment.yml b/modules/nf-core/pigz/compress/environment.yml index 7551d187..b586f5be 100644 --- a/modules/nf-core/pigz/compress/environment.yml +++ b/modules/nf-core/pigz/compress/environment.yml @@ -4,6 +4,5 @@ name: "pigz_compress" channels: - conda-forge - bioconda - - defaults dependencies: - "pigz=2.8" diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index bd57cb54..610077d9 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -2,7 +2,6 @@ name: samtools_flagstat channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.19.2 - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index a5e50649..2b16cd61 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -2,7 +2,6 @@ name: samtools_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.19.2 - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml index b0676f33..e8dee97c 100644 --- a/modules/nf-core/samtools/view/environment.yml +++ b/modules/nf-core/samtools/view/environment.yml @@ -2,7 +2,6 @@ name: samtools_view channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.19.2 - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/seqtk/subseq/environment.yml b/modules/nf-core/seqtk/subseq/environment.yml index 7abe3644..69c1fcfd 100644 --- a/modules/nf-core/seqtk/subseq/environment.yml +++ b/modules/nf-core/seqtk/subseq/environment.yml @@ -2,6 +2,5 @@ name: seqtk_subseq channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::seqtk=1.4 diff --git a/modules/nf-core/windowmasker/mkcounts/environment.yml b/modules/nf-core/windowmasker/mkcounts/environment.yml index e4d72108..8aca82f5 100644 --- a/modules/nf-core/windowmasker/mkcounts/environment.yml +++ b/modules/nf-core/windowmasker/mkcounts/environment.yml @@ -2,6 +2,5 @@ name: windowmasker_mkcounts channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::blast=2.15.0 diff --git a/modules/nf-core/windowmasker/ustat/environment.yml b/modules/nf-core/windowmasker/ustat/environment.yml index b83d82e5..437de1e5 100644 --- a/modules/nf-core/windowmasker/ustat/environment.yml +++ b/modules/nf-core/windowmasker/ustat/environment.yml @@ -2,6 +2,5 @@ name: windowmasker_ustat channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::blast=2.15.0