Some changes are not shown.
.reuse/dep5
0 → 100644LICENSE
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
LICENSES/AGPL-3.0-or-later.txt
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
LICENSES/CC-BY-SA-4.0.txt
0 → 100644bin/.gitignore
0 → 100644doc/Makefile
deleted100644 → 0doc/TP_computational_biologists.md
deleted100644 → 0doc/TP_experimental_biologists.md
deleted100644 → 0doc/building_your_pipeline.md
0 → 100644doc/getting_started.md
0 → 100644doc/img/fork.png.license
0 → 100644doc/img/merge_request.png.license
0 → 100644doc/img/webide.png.license
0 → 100644doc/mail.txt
0 → 100644doc/mail.txt.license
0 → 100644doc/nf_projects.md
0 → 100644results/.gitignore
0 → 100644src/.docker_modules/docker_push.sh
0 → 100755src/.docker_modules/docker_update.sh
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File changed and moved.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File changed and moved.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File changed and moved.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File changed and moved.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File changed and moved.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
src/.docker_modules/kb/0.26.0/Dockerfile
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
src/.docker_modules/kb/0.26.0/fix_t2g.py
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/.docker_modules/kb/0.26.0/t2g.py
0 → 100755File added.
Preview size limit exceeded, changes collapsed.
src/.docker_modules/kb/0.26.3/Dockerfile
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
src/.docker_modules/kb/0.26.3/t2g.py
0 → 100755File added.
Preview size limit exceeded, changes collapsed.
src/.docker_modules/last/1060/Dockerfile
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File changed and moved.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File changed and moved.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File changed and moved.
Preview size limit exceeded, changes collapsed.
File changed and moved.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File changed and moved.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File changed and moved.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File changed and moved.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File changed and moved.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File changed and moved.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
src/.docker_modules/sanity/Dockerfile
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File changed and moved.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File changed and moved.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
src/.docker_modules/ucsc/375/Dockerfile
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
src/.docker_modules/ucsc/400/Dockerfile
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
src/.docker_modules/ucsc/407/Dockerfile
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
src/.docker_modules/ucsc/407/gtf2bed.pl
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File changed and moved.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
src/.singularity_in2p3
0 → 120000File added.
Preview size limit exceeded, changes collapsed.
src/.singularity_psmn
0 → 120000File added.
Preview size limit exceeded, changes collapsed.
src/docker_modules/BEDtools/2.25.0/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/BWA/0.7.17/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/Bowtie/1.2.2/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/Bowtie2/2.3.4.1/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/FastQC/0.11.5/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/GATK/4.0.8.1/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/HISAT2/2.0.0/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/HTSeq/0.8.0/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/Kallisto/0.43.1/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/Kallisto/0.44.0/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/MACS2/2.1.0/Dockerfile
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/MACS2/2.1.0/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/MUSIC/6613c53/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/MultiQC/1.0/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/RSEM/1.3.0/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/SAMtools/1.7/Dockerfile
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/SAMtools/1.7/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/SRAtoolkit/2.8.2/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/Salmon/0.8.2/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/TopHat/2.1.1/Dockerfile
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/TopHat/2.1.1/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/Trimmomatic/0.36/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/UrQt/d62c1f8/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/bcftools/1.7/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/bioawk/1.0/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/canu/1.6/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/cutadapt/1.14/Dockerfile
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/cutadapt/1.14/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/deepTools/3.0.2/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/file_handle/0.1.1/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/picard/2.18.11/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/pigz/2.4/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/sambamba/0.6.7/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/docker_modules/samblaster/0.1.24/docker_init.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/example_chipseq.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/example_marseq.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/example_variant_calling.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/fasta_sampler.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/in2p3.pbs
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
File changed.
Preview size limit exceeded, changes collapsed.
src/nextflow.config
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/BEDtools/fasta_from_bed.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/BEDtools/fasta_from_bed.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/BEDtools/tests.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/BWA/indexing.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/BWA/indexing.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/BWA/mapping_paired.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/BWA/mapping_paired.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/BWA/tests.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/Bowtie/indexing.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/Bowtie/indexing.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/Bowtie/mapping_paired.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/Bowtie/mapping_paired.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/Bowtie/mapping_single.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/Bowtie/mapping_single.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/Bowtie/tests.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/Bowtie2/indexing.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/Bowtie2/indexing.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/Bowtie2/mapping_paired.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/Bowtie2/mapping_paired.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/Bowtie2/mapping_single.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/Bowtie2/mapping_single.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/Bowtie2/tests.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/FastQC/fastqc_paired.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/FastQC/fastqc_paired.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/FastQC/fastqc_single.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/FastQC/fastqc_single.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/FastQC/tests.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/HTSeq/htseq.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/HTSeq/htseq.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/HTSeq/tests.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/Kallisto/indexing.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/Kallisto/indexing.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/Kallisto/mapping_paired.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/Kallisto/mapping_paired.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/Kallisto/mapping_single.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/Kallisto/mapping_single.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/Kallisto/tests.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/MUSIC/peak_calling_single.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/MUSIC/peak_calling_single.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/MUSIC/tests.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/MultiQC/multiqc_paired.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/MultiQC/multiqc_paired.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/MultiQC/multiqc_single.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/MultiQC/multiqc_single.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/MultiQC/tests.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/RSEM/indexing.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/RSEM/indexing.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/RSEM/quantification_paired.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/RSEM/quantification_paired.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/RSEM/quantification_single.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/RSEM/quantification_single.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/RSEM/tests.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/SAMtools/filter_bams.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/SAMtools/filter_bams.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/SAMtools/index_bams.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/SAMtools/index_bams.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/SAMtools/sort_bams.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/SAMtools/sort_bams.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/SAMtools/split_bams.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/SAMtools/split_bams.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/SAMtools/tests.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/SRAtoolkit/fastqdump.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/SRAtoolkit/fastqdump.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/SRAtoolkit/tests.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/UrQt/tests.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/UrQt/trimming_paired.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/UrQt/trimming_paired.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/UrQt/trimming_single.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/UrQt/trimming_single.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/UrQt/urqt.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/agat/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/alntools/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/beagle/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/bedtools/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/bioawk/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/bioconvert/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/bowtie/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/bowtie2/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/bwa/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/cellphonedb/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/cutadapt/adaptor_removal_paired.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/cutadapt/adaptor_removal_paired.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/cutadapt/adaptor_removal_single.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/cutadapt/adaptor_removal_single.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/cutadapt/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/cutadapt/tests.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/cutadapt/trimming_paired.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/cutadapt/trimming_paired.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/cutadapt/trimming_single.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/cutadapt/trimming_single.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/danpos/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/deeptools/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/emase-zero/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/emase/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/fastp/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/fastq_screen/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/fastqc/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/flexi_splitter/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/g2gtools/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/gatk3/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/gatk4/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/gffread/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/guppy-cpu/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/guppy-gpu/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/hisat2/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/htseq/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/kallisto/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/kb/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/macs2/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/macs3/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/minimap2/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/multiqc/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/picard/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/porechop/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/rasusa/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/rasusa/test.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/rasusa/test.sh
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/salmon/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/sambamba/index_bams.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/sambamba/index_bams.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/sambamba/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/sambamba/sort_bams.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/sambamba/sort_bams.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/sambamba/split_bams.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/sambamba/split_bams.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/sambamba/tests.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/samblaster/dedup_sams.config
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/samblaster/dedup_sams.nf
deleted100644 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/samblaster/tests.sh
deleted100755 → 0File deleted.
Preview size limit exceeded, changes collapsed.
src/nf_modules/samtools/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/sanity/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
File moved.
File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/sratoolkit/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/star/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/stringtie2/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/trinity/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/ucsc/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
src/nf_modules/urqt/main.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
sge_modules @ 1d6cfb91
File deleted.
Preview size limit exceeded, changes collapsed.
src/solution_RNASeq.nf
0 → 100644File added.
Preview size limit exceeded, changes collapsed.
File changed.
Preview size limit exceeded, changes collapsed.
File changed.
Preview size limit exceeded, changes collapsed.