update modules to include software licenses, if possible #873
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potential source of license identifier keys: https://spdx.org/licenses/ |
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license ambiguities:
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minor linguistic ambiguity: license or licence? I've gone for latter given large Old World user base for nf-core |
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no SPDX license key for US Government Works, which applies to licenses for, e.g. will coin key |
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Is your feature request related to a problem? Please describe
several modules are missing software licenses in
meta.ymlDescribe the solution you'd like
modules should have a
licenseline inmeta.yml, e.g.Describe alternatives you've considered
could leave things well alone since the status quo does not seem to bother anybody (yet?)
Additional context
some software, such as
picardorrseqc, is represented in multiple modules but most likely governed under the same license. not sure how to enforce this, or if it's even worthwhile.not sure how to handle software with NO license
here is the (long!) list of modules that require updates:
*
cat/cat/meta.yml*
cat/fastq/meta.yml*
rseqc/readdistribution/meta.yml*
rseqc/junctionsaturation/meta.yml*
rseqc/readduplication/meta.yml*
rseqc/inferexperiment/meta.yml*
rseqc/bamstat/meta.yml*
rseqc/innerdistance/meta.yml*
rseqc/junctionannotation/meta.yml*
tabix/tabix/meta.yml*
tabix/bgziptabix/meta.yml*
tabix/bgzip/meta.yml*
picard/sortsam/meta.yml*
picard/collectmultiplemetrics/meta.yml*
picard/markduplicates/meta.yml*
picard/mergesamfiles/meta.yml*
picard/collectwgsmetrics/meta.yml*
tiddit/sv/meta.yml*
qualimap/bamqc/meta.yml*
rsem/calculateexpression/meta.yml*
rsem/preparereference/meta.yml*
bwameth/align/meta.yml*
bwameth/index/meta.yml*
nanolyse/meta.yml*
cutadapt/meta.yml*
multiqc/meta.yml*
bowtie2/align/meta.yml*
bowtie2/build/meta.yml*
stringtie/stringtie/meta.yml*
stringtie/merge/meta.yml*
untar/meta.yml*
mosdepth/meta.yml*
dshbio/filtergff3/meta.yml*
dshbio/splitgff3/meta.yml*
dshbio/splitbed/meta.yml*
dshbio/filterbed/meta.yml*
dshbio/exportsegments/meta.yml*
homer/annotatepeaks/meta.yml*
homer/findpeaks/meta.yml*
homer/makeucscfile/meta.yml*
homer/maketagdirectory/meta.yml*
bcftools/concat/meta.yml*
bcftools/consensus/meta.yml*
bcftools/merge/meta.yml*
bcftools/mpileup/meta.yml*
bcftools/norm/meta.yml*
bcftools/view/meta.yml*
bcftools/filter/meta.yml*
bcftools/query/meta.yml*
bcftools/stats/meta.yml*
bcftools/isec/meta.yml*
graphmap2/align/meta.yml*
graphmap2/index/meta.yml*
bwamem2/index/meta.yml*
bwamem2/mem/meta.yml*
methyldackel/mbias/meta.yml*
methyldackel/extract/meta.yml*
bismark/methylationextractor/meta.yml*
bismark/align/meta.yml*
bismark/genomepreparation/meta.yml*
bismark/report/meta.yml*
bismark/deduplicate/meta.yml*
bismark/summary/meta.yml*
pangolin/meta.yml*
trimgalore/meta.yml*
minimap2/align/meta.yml*
minimap2/index/meta.yml*
snpsites/meta.yml*
cnvkit/meta.yml*
minia/meta.yml*
ensemblvep/meta.yml*
gubbins/meta.yml*
snpeff/meta.yml*
bwa/index/meta.yml*
bwa/mem/meta.yml*
bowtie/align/meta.yml*
bowtie/build/meta.yml*
nanoplot/meta.yml*
star/genomegenerate/meta.yml*
star/align/meta.yml*
seqwish/induce/meta.yml*
bedtools/complement/meta.yml*
bedtools/maskfasta/meta.yml*
bedtools/intersect/meta.yml*
bedtools/sort/meta.yml*
bedtools/subtract/meta.yml*
bedtools/merge/meta.yml*
bedtools/slop/meta.yml*
bedtools/genomecov/meta.yml*
bedtools/getfasta/meta.yml*
bedtools/bamtobed/meta.yml*
qcat/meta.yml*
quast/meta.yml*
blast/makeblastdb/meta.yml*
blast/blastn/meta.yml*
kraken2/kraken2/meta.yml*
fastqc/meta.yml*
samtools/sort/meta.yml*
samtools/merge/meta.yml*
samtools/mpileup/meta.yml*
samtools/idxstats/meta.yml*
samtools/ampliconclip/meta.yml*
samtools/faidx/meta.yml*
samtools/view/meta.yml*
samtools/index/meta.yml*
samtools/flagstat/meta.yml*
samtools/fastq/meta.yml*
samtools/stats/meta.yml*
ivar/consensus/meta.yml*
ivar/variants/meta.yml*
ivar/trim/meta.yml*
custom/dumpsoftwareversions/meta.yml*
gatk4/mergebamalignment/meta.yml*
gatk4/variantfiltration/meta.yml*
gatk4/calculatecontamination/meta.yml*
gatk4/learnreadorientationmodel/meta.yml*
gatk4/samtofastq/meta.yml*
gatk4/getpileupsummaries/meta.yml*
gatk4/createsequencedictionary/meta.yml*
gatk4/splitncigarreads/meta.yml*
gatk4/haplotypecaller/meta.yml*
gatk4/intervallisttools/meta.yml*
gatk4/baserecalibrator/meta.yml*
gatk4/applybqsr/meta.yml*
gatk4/revertsam/meta.yml*
gatk4/bedtointervallist/meta.yml*
gatk4/mergevcfs/meta.yml*
gatk4/mutect2/meta.yml*
seacr/callpeak/meta.yml*
seqkit/split2/meta.yml*
fastp/meta.yml*
salmon/quant/meta.yml*
salmon/index/meta.yml*
bandage/image/meta.yml*
sequenzautils/gcwiggle/meta.yml*
sequenzautils/bam2seqz/meta.yml*
gunzip/meta.ymlThe text was updated successfully, but these errors were encountered: