mirror of
https://github.com/MillironX/nf-core_modules.git
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4ec8b025bd
* 📦 NEW: Add module lima * 👌 IMPROVE: Move .pbi output to reports channel * 🐛 FIX: Fix report channel definition * 👌IMPROVE; Remove options from command line update test script with removed options * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 🐛 FIX: Add pbi input * 👌 IMPROVE: Add parallelization to lima * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The accept one channel (primers move into the first channel) * 👌 IMPROVE: Assign a value channel for pimers Improve code workflow readability * 👌 IMPROVE: Update .gitignore * 👌 IMPROVE: Update module to last template version * 🐛 FIX: Correct Singularity and Docker URL * 👌 IMPROVE: Update to the last version of modules template * 👌 IMPROVE: Update test_data.config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 🐛 FIX: Fill contains args * 📦 NEW: Add module lima * 👌 IMPROVE: Move .pbi output to reports channel * 🐛 FIX: Fix report channel definition * 👌IMPROVE; Remove options from command line update test script with removed options * 🐛 FIX: Add pbi input * 👌 IMPROVE: Add parallelization to lima * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The accept one channel (primers move into the first channel) * 👌 IMPROVE: Assign a value channel for pimers Improve code workflow readability * 👌 IMPROVE: Update .gitignore * 👌 IMPROVE: Update module to last template version * 🐛 FIX: Correct Singularity and Docker URL * 👌 IMPROVE: Update to the last version of modules template * 👌 IMPROVE: Update test_data.config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 🐛 FIX: Fill contains args * 👌 IMPROVE: Add channel for each output * 👌 IMPROVE: Remove comments * 📦 NEW: Add module lima * 👌 IMPROVE: Move .pbi output to reports channel * 🐛 FIX: Fix report channel definition * 👌IMPROVE; Remove options from command line update test script with removed options * 🐛 FIX: Add pbi input * 👌 IMPROVE: Add parallelization to lima * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The accept one channel (primers move into the first channel) * 👌 IMPROVE: Assign a value channel for pimers Improve code workflow readability * 👌 IMPROVE: Update module to last template version * 🐛 FIX: Correct Singularity and Docker URL * 👌 IMPROVE: Update to the last version of modules template * 👌 IMPROVE: Update test_data.config * 👌 IMPROVE: Remove pbi from input files * 🐛 FIX: Fill contains args * 📦 NEW: Add module lima * 👌 IMPROVE: Move .pbi output to reports channel * 🐛 FIX: Fix report channel definition * 👌IMPROVE; Remove options from command line update test script with removed options * 🐛 FIX: Add pbi input * 👌 IMPROVE: Add parallelization to lima * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The accept one channel (primers move into the first channel) * 👌 IMPROVE: Assign a value channel for pimers Improve code workflow readability * 👌 IMPROVE: Update module to last template version * 🐛 FIX: Correct Singularity and Docker URL * 👌 IMPROVE: Update to the last version of modules template * 👌 IMPROVE: Update test_data.config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 🐛 FIX: Fill contains args * 👌 IMPROVE: Add channel for each output * 👌 IMPROVE: Remove comments * 🐛 FIX: Clean test_data.config * Update modules/lima/main.nf Add meta to each output Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/lima/main.nf Remove useless parenthesis Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * 🐛 FIX: Keep version number only * 🐛 FIX: Reintegrate prefix variable and use it to define output file name * 👌 IMPROVE: add suffix arg to check output files names * 👌 IMPROVE: Use prefix for output filename * 🐛 FIX: Set optional output Allow usage of different input formats * 👌 IMPROVE: Update meta file * 👌 IMPROVE: Update test One test for each input file type * 👌 IMPROVE: add fasta, fastq.gz, fastq, fastq.gz test files * 👌 IMPROVE: Update with last templates / Follow new version.yaml rule * 🐛 FIX: Fix typos and include getProcessName function * 👌 IMPROVE: Update .gitignore * 👌 IMPROVE: Using suffix to manage output was not a my best idea Add a bash code to detect extension and update output file name * 👌 IMPROVE: clean code Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> |
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| .. | ||
| abacas | ||
| adapterremoval | ||
| agrvate | ||
| allelecounter | ||
| arriba | ||
| artic | ||
| bamaligncleaner | ||
| bandage/image | ||
| bbmap | ||
| bcftools | ||
| bedtools | ||
| bismark | ||
| blast | ||
| bowtie | ||
| bowtie2 | ||
| bwa | ||
| bwamem2 | ||
| bwameth | ||
| cat | ||
| chromap | ||
| cnvkit | ||
| cooler | ||
| cutadapt | ||
| damageprofiler | ||
| deeptools | ||
| delly/call | ||
| diamond | ||
| dragonflye | ||
| dshbio | ||
| ensemblvep | ||
| expansionhunter | ||
| fastani | ||
| fastp | ||
| fastqc | ||
| fasttree | ||
| fgbio | ||
| flash | ||
| gatk4 | ||
| genmap | ||
| gffread | ||
| glnexus | ||
| graphmap2 | ||
| gubbins | ||
| gunzip | ||
| hifiasm | ||
| hisat2 | ||
| hmmer/hmmalign | ||
| homer | ||
| iqtree | ||
| ivar | ||
| kallisto/index | ||
| kallistobustools | ||
| kleborate | ||
| kraken2/kraken2 | ||
| last | ||
| lib | ||
| lima | ||
| lofreq | ||
| macs2/callpeak | ||
| malt | ||
| maltextract | ||
| mash/sketch | ||
| metaphlan3 | ||
| methyldackel | ||
| minia | ||
| minimap2 | ||
| mosdepth | ||
| msisensor | ||
| multiqc | ||
| muscle | ||
| nanolyse | ||
| nanoplot | ||
| nextclade | ||
| optitype | ||
| pairix | ||
| pairtools | ||
| pangolin | ||
| pbccs | ||
| phantompeakqualtools | ||
| picard | ||
| plasmidid | ||
| plink/vcf | ||
| preseq/lcextrap | ||
| prodigal | ||
| prokka | ||
| pycoqc | ||
| pydamage | ||
| qcat | ||
| qualimap | ||
| quast | ||
| rapidnj | ||
| rasusa | ||
| raxmlng | ||
| rsem | ||
| rseqc | ||
| salmon | ||
| samtools | ||
| seacr/callpeak | ||
| seqkit/split2 | ||
| seqtk | ||
| sequenzautils | ||
| seqwish/induce | ||
| shovill | ||
| snpdists | ||
| snpeff | ||
| snpsites | ||
| sortmerna | ||
| spades | ||
| staphopiasccmec | ||
| star | ||
| strelka/germline | ||
| stringtie | ||
| subread/featurecounts | ||
| tabix | ||
| tiddit/sv | ||
| trimgalore | ||
| ucsc | ||
| umitools | ||
| unicycler | ||
| untar | ||
| unzip | ||
| variantbam | ||
| vcftools | ||
| yara | ||