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updating BioNF
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@lucacozzuto
lucacozzuto committed Oct 1, 2024
1 parent bcbe81e commit c6ee7e1
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion BioNextflow
Submodule BioNextflow updated 88 files
+2 −0 .gitignore
+1 −1 README.md
+8 −0 docker_files/Dockerfile_alevinqc_0.1
+0 −23 docker_files/Dockerfile_anno
+31 −0 docker_files/Dockerfile_falco
+32 −0 docker_files/Dockerfile_nanoplot_1.42.0
+49 −0 docker_files/Dockerfile_racon1.5.0
+19 −0 docker_files/Dockerfile_seurat_4.1
+9 −0 docker_files/pod5/Dockerfile
+9 −0 docker_files/pod5/Dockerfile_0.2.4
+9 −0 docker_files/pod5/Dockerfile_0.3.11
+7 −0 docker_files/pod5/environment.yml
+7 −0 docker_files/pod5/environment_0.2.4.yml
+7 −0 docker_files/pod5/environment_0.3.11.yml
+13 −11 example_pipe/main.nf
+15 −13 example_pipe/main2.nf
+11 −0 scripts/README.md
+49 −0 scripts/get_singularity.py
+154 −0 subworkflows/alignment/biscuit.nf
+150 −0 subworkflows/alignment/bismark.nf
+123 −0 subworkflows/alignment/bowtie2.nf
+26 −1 subworkflows/alignment/bwa.nf
+8 −1 subworkflows/alignment/minimap2.nf
+74 −17 subworkflows/alignment/salmon.nf
+26 −11 subworkflows/alignment/star.nf
+112 −0 subworkflows/alignment/winnowmap.nf
+111 −0 subworkflows/allele_specific/snpsplit.nf
+189 −0 subworkflows/basecalling/dorado.nf
+245 −16 subworkflows/basecalling/guppy.nf
+75 −0 subworkflows/chem_modification/epinano_1.2.4.nf
+137 −0 subworkflows/chem_modification/modphred.nf
+11 −2 subworkflows/chem_modification/tailfindr.nf
+88 −0 subworkflows/demultiplexing/bcl2fastq.nf
+79 −0 subworkflows/demultiplexing/readucks.nf
+70 −0 subworkflows/demultiplexing/seq_tagger.nf
+70 −8 subworkflows/global_functions.nf
+ − subworkflows/immune_sys/._trust4.nf
+101 −0 subworkflows/immune_sys/trust4.nf
+136 −0 subworkflows/metagenomics/bracken.nf
+94 −0 subworkflows/metagenomics/kaiju.nf
+73 −26 subworkflows/metagenomics/kraken2.nf
+66 −0 subworkflows/misc/bedclip.nf
+65 −0 subworkflows/misc/bedtobigbed.nf
+98 −0 subworkflows/misc/bedtools.nf
+421 −0 subworkflows/misc/deeptools.nf
+230 −0 subworkflows/misc/demulti_fast5.nf
+65 −0 subworkflows/misc/demulti_fastq.nf
+136 −0 subworkflows/misc/demulti_pod5.nf
+137 −1 subworkflows/misc/misc.nf
+63 −2 subworkflows/misc/picard.nf
+272 −7 subworkflows/misc/samtools.nf
+30 −0 subworkflows/motif_analysis/homer.nf
+2 −2 subworkflows/peak_calling/epic.nf
+2 −3 subworkflows/peak_calling/epic2.nf
+101 −0 subworkflows/peak_calling/exomePeak2.nf
+63 −0 subworkflows/peak_calling/genrich.nf
+72 −0 subworkflows/peak_calling/macs3.nf
+161 −0 subworkflows/peak_calling/seacr.nf
+74 −0 subworkflows/qc/alevinqc.nf
+65 −0 subworkflows/qc/falco.nf
+64 −0 subworkflows/qc/fastq_screen.nf
+37 −1 subworkflows/qc/fastqc.nf
+5 −5 subworkflows/qc/nanoplot.nf
+63 −0 subworkflows/qc/qualimap.nf
+126 −0 subworkflows/qc/ribodetector.nf
+9 −12 subworkflows/read_count/htseq.nf
+95 −0 subworkflows/read_count/subread.nf
+70 −4 subworkflows/reporting/multiqc.nf
+149 −0 subworkflows/single_cell/cellranger.nf
+360 −0 subworkflows/single_cell/seurat.nf
+145 −0 subworkflows/single_cell/spipe.nf
+ − subworkflows/smallrnas/._trax.nf
+166 −0 subworkflows/smallrnas/trax.nf
+68 −0 subworkflows/snp_calling/bcftools.nf
+83 −0 subworkflows/snp_calling/clairS.nf
+85 −0 subworkflows/snp_calling/clairS_TO.nf
+102 −0 subworkflows/structural_variant/sniffles.nf
+72 −0 subworkflows/trimming/cutadapt.nf
+35 −1 subworkflows/trimming/nanoq.nf
+22 −7 subworkflows/trimming/skewer.nf
+122 −8 subworkflows/trimming/trimmomatic.nf
+79 −0 subworkflows/var_annotation/snpeff.nf
+72 −0 subworkflows/var_annotation/snpsift.nf
+64 −0 workflows/aligner.nf
+81 −0 workflows/basecaller.nf
+79 −0 workflows/basecaller_demultiplexer.nf
+50 −0 workflows/demultiplexer.nf
+122 −0 workflows/peakcaller.nf

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