From 705226a9482733c67c18c799cfe394cf7af2ecda Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 5 Jun 2018 16:14:47 +0200
Subject: [PATCH] mv nf files to nf_modules

---
 src/{docker_modules => nf_modules}/Bowtie2/bowtie2.config         | 0
 src/{docker_modules => nf_modules}/Bowtie2/bowtie2.nf             | 0
 src/{docker_modules => nf_modules}/Bowtie2/tests/index.nf         | 0
 .../Bowtie2/tests/mapping_paired.nf                               | 0
 .../Bowtie2/tests/mapping_single.nf                               | 0
 src/{docker_modules => nf_modules}/HTSeq/htseq.config             | 0
 src/{docker_modules => nf_modules}/HTSeq/htseq.nf                 | 0
 src/{docker_modules => nf_modules}/HTSeq/tests/counting.nf        | 0
 src/{docker_modules => nf_modules}/Kallisto/kallisto.config       | 0
 src/{docker_modules => nf_modules}/Kallisto/kallisto.nf           | 0
 src/{docker_modules => nf_modules}/Kallisto/tests/index.nf        | 0
 .../Kallisto/tests/mapping_paired.nf                              | 0
 .../Kallisto/tests/mapping_single.nf                              | 0
 src/{docker_modules => nf_modules}/RSEM/rsem.config               | 0
 src/{docker_modules => nf_modules}/RSEM/rsem.nf                   | 0
 src/{docker_modules => nf_modules}/RSEM/tests/index.nf            | 0
 .../RSEM/tests/quantification_paired.nf                           | 0
 .../RSEM/tests/quantification_single.nf                           | 0
 src/{docker_modules => nf_modules}/SAMtools/samtools.config       | 0
 src/{docker_modules => nf_modules}/SAMtools/samtools.nf           | 0
 src/{docker_modules => nf_modules}/SAMtools/tests/filter_bams.nf  | 0
 src/{docker_modules => nf_modules}/SAMtools/tests/index_bams.nf   | 0
 src/{docker_modules => nf_modules}/SAMtools/tests/sort_bams.nf    | 0
 src/{docker_modules => nf_modules}/SAMtools/tests/split_bams.nf   | 0
 src/{docker_modules => nf_modules}/UrQt/tests/trimming_paired.nf  | 0
 src/{docker_modules => nf_modules}/UrQt/tests/trimming_single.nf  | 0
 src/{docker_modules => nf_modules}/UrQt/urqt.config               | 0
 src/{docker_modules => nf_modules}/UrQt/urqt.nf                   | 0
 src/{docker_modules => nf_modules}/cutadapt/cutadapt.config       | 0
 src/{docker_modules => nf_modules}/cutadapt/cutadapt.nf           | 0
 .../cutadapt/tests/adaptor_removal_paired.nf                      | 0
 .../cutadapt/tests/adaptor_removal_single.nf                      | 0
 .../cutadapt/tests/trimming_paired.nf                             | 0
 .../cutadapt/tests/trimming_single.nf                             | 0
 34 files changed, 0 insertions(+), 0 deletions(-)
 rename src/{docker_modules => nf_modules}/Bowtie2/bowtie2.config (100%)
 rename src/{docker_modules => nf_modules}/Bowtie2/bowtie2.nf (100%)
 rename src/{docker_modules => nf_modules}/Bowtie2/tests/index.nf (100%)
 rename src/{docker_modules => nf_modules}/Bowtie2/tests/mapping_paired.nf (100%)
 rename src/{docker_modules => nf_modules}/Bowtie2/tests/mapping_single.nf (100%)
 rename src/{docker_modules => nf_modules}/HTSeq/htseq.config (100%)
 rename src/{docker_modules => nf_modules}/HTSeq/htseq.nf (100%)
 rename src/{docker_modules => nf_modules}/HTSeq/tests/counting.nf (100%)
 rename src/{docker_modules => nf_modules}/Kallisto/kallisto.config (100%)
 rename src/{docker_modules => nf_modules}/Kallisto/kallisto.nf (100%)
 rename src/{docker_modules => nf_modules}/Kallisto/tests/index.nf (100%)
 rename src/{docker_modules => nf_modules}/Kallisto/tests/mapping_paired.nf (100%)
 rename src/{docker_modules => nf_modules}/Kallisto/tests/mapping_single.nf (100%)
 rename src/{docker_modules => nf_modules}/RSEM/rsem.config (100%)
 rename src/{docker_modules => nf_modules}/RSEM/rsem.nf (100%)
 rename src/{docker_modules => nf_modules}/RSEM/tests/index.nf (100%)
 rename src/{docker_modules => nf_modules}/RSEM/tests/quantification_paired.nf (100%)
 rename src/{docker_modules => nf_modules}/RSEM/tests/quantification_single.nf (100%)
 rename src/{docker_modules => nf_modules}/SAMtools/samtools.config (100%)
 rename src/{docker_modules => nf_modules}/SAMtools/samtools.nf (100%)
 rename src/{docker_modules => nf_modules}/SAMtools/tests/filter_bams.nf (100%)
 rename src/{docker_modules => nf_modules}/SAMtools/tests/index_bams.nf (100%)
 rename src/{docker_modules => nf_modules}/SAMtools/tests/sort_bams.nf (100%)
 rename src/{docker_modules => nf_modules}/SAMtools/tests/split_bams.nf (100%)
 rename src/{docker_modules => nf_modules}/UrQt/tests/trimming_paired.nf (100%)
 rename src/{docker_modules => nf_modules}/UrQt/tests/trimming_single.nf (100%)
 rename src/{docker_modules => nf_modules}/UrQt/urqt.config (100%)
 rename src/{docker_modules => nf_modules}/UrQt/urqt.nf (100%)
 rename src/{docker_modules => nf_modules}/cutadapt/cutadapt.config (100%)
 rename src/{docker_modules => nf_modules}/cutadapt/cutadapt.nf (100%)
 rename src/{docker_modules => nf_modules}/cutadapt/tests/adaptor_removal_paired.nf (100%)
 rename src/{docker_modules => nf_modules}/cutadapt/tests/adaptor_removal_single.nf (100%)
 rename src/{docker_modules => nf_modules}/cutadapt/tests/trimming_paired.nf (100%)
 rename src/{docker_modules => nf_modules}/cutadapt/tests/trimming_single.nf (100%)

diff --git a/src/docker_modules/Bowtie2/bowtie2.config b/src/nf_modules/Bowtie2/bowtie2.config
similarity index 100%
rename from src/docker_modules/Bowtie2/bowtie2.config
rename to src/nf_modules/Bowtie2/bowtie2.config
diff --git a/src/docker_modules/Bowtie2/bowtie2.nf b/src/nf_modules/Bowtie2/bowtie2.nf
similarity index 100%
rename from src/docker_modules/Bowtie2/bowtie2.nf
rename to src/nf_modules/Bowtie2/bowtie2.nf
diff --git a/src/docker_modules/Bowtie2/tests/index.nf b/src/nf_modules/Bowtie2/tests/index.nf
similarity index 100%
rename from src/docker_modules/Bowtie2/tests/index.nf
rename to src/nf_modules/Bowtie2/tests/index.nf
diff --git a/src/docker_modules/Bowtie2/tests/mapping_paired.nf b/src/nf_modules/Bowtie2/tests/mapping_paired.nf
similarity index 100%
rename from src/docker_modules/Bowtie2/tests/mapping_paired.nf
rename to src/nf_modules/Bowtie2/tests/mapping_paired.nf
diff --git a/src/docker_modules/Bowtie2/tests/mapping_single.nf b/src/nf_modules/Bowtie2/tests/mapping_single.nf
similarity index 100%
rename from src/docker_modules/Bowtie2/tests/mapping_single.nf
rename to src/nf_modules/Bowtie2/tests/mapping_single.nf
diff --git a/src/docker_modules/HTSeq/htseq.config b/src/nf_modules/HTSeq/htseq.config
similarity index 100%
rename from src/docker_modules/HTSeq/htseq.config
rename to src/nf_modules/HTSeq/htseq.config
diff --git a/src/docker_modules/HTSeq/htseq.nf b/src/nf_modules/HTSeq/htseq.nf
similarity index 100%
rename from src/docker_modules/HTSeq/htseq.nf
rename to src/nf_modules/HTSeq/htseq.nf
diff --git a/src/docker_modules/HTSeq/tests/counting.nf b/src/nf_modules/HTSeq/tests/counting.nf
similarity index 100%
rename from src/docker_modules/HTSeq/tests/counting.nf
rename to src/nf_modules/HTSeq/tests/counting.nf
diff --git a/src/docker_modules/Kallisto/kallisto.config b/src/nf_modules/Kallisto/kallisto.config
similarity index 100%
rename from src/docker_modules/Kallisto/kallisto.config
rename to src/nf_modules/Kallisto/kallisto.config
diff --git a/src/docker_modules/Kallisto/kallisto.nf b/src/nf_modules/Kallisto/kallisto.nf
similarity index 100%
rename from src/docker_modules/Kallisto/kallisto.nf
rename to src/nf_modules/Kallisto/kallisto.nf
diff --git a/src/docker_modules/Kallisto/tests/index.nf b/src/nf_modules/Kallisto/tests/index.nf
similarity index 100%
rename from src/docker_modules/Kallisto/tests/index.nf
rename to src/nf_modules/Kallisto/tests/index.nf
diff --git a/src/docker_modules/Kallisto/tests/mapping_paired.nf b/src/nf_modules/Kallisto/tests/mapping_paired.nf
similarity index 100%
rename from src/docker_modules/Kallisto/tests/mapping_paired.nf
rename to src/nf_modules/Kallisto/tests/mapping_paired.nf
diff --git a/src/docker_modules/Kallisto/tests/mapping_single.nf b/src/nf_modules/Kallisto/tests/mapping_single.nf
similarity index 100%
rename from src/docker_modules/Kallisto/tests/mapping_single.nf
rename to src/nf_modules/Kallisto/tests/mapping_single.nf
diff --git a/src/docker_modules/RSEM/rsem.config b/src/nf_modules/RSEM/rsem.config
similarity index 100%
rename from src/docker_modules/RSEM/rsem.config
rename to src/nf_modules/RSEM/rsem.config
diff --git a/src/docker_modules/RSEM/rsem.nf b/src/nf_modules/RSEM/rsem.nf
similarity index 100%
rename from src/docker_modules/RSEM/rsem.nf
rename to src/nf_modules/RSEM/rsem.nf
diff --git a/src/docker_modules/RSEM/tests/index.nf b/src/nf_modules/RSEM/tests/index.nf
similarity index 100%
rename from src/docker_modules/RSEM/tests/index.nf
rename to src/nf_modules/RSEM/tests/index.nf
diff --git a/src/docker_modules/RSEM/tests/quantification_paired.nf b/src/nf_modules/RSEM/tests/quantification_paired.nf
similarity index 100%
rename from src/docker_modules/RSEM/tests/quantification_paired.nf
rename to src/nf_modules/RSEM/tests/quantification_paired.nf
diff --git a/src/docker_modules/RSEM/tests/quantification_single.nf b/src/nf_modules/RSEM/tests/quantification_single.nf
similarity index 100%
rename from src/docker_modules/RSEM/tests/quantification_single.nf
rename to src/nf_modules/RSEM/tests/quantification_single.nf
diff --git a/src/docker_modules/SAMtools/samtools.config b/src/nf_modules/SAMtools/samtools.config
similarity index 100%
rename from src/docker_modules/SAMtools/samtools.config
rename to src/nf_modules/SAMtools/samtools.config
diff --git a/src/docker_modules/SAMtools/samtools.nf b/src/nf_modules/SAMtools/samtools.nf
similarity index 100%
rename from src/docker_modules/SAMtools/samtools.nf
rename to src/nf_modules/SAMtools/samtools.nf
diff --git a/src/docker_modules/SAMtools/tests/filter_bams.nf b/src/nf_modules/SAMtools/tests/filter_bams.nf
similarity index 100%
rename from src/docker_modules/SAMtools/tests/filter_bams.nf
rename to src/nf_modules/SAMtools/tests/filter_bams.nf
diff --git a/src/docker_modules/SAMtools/tests/index_bams.nf b/src/nf_modules/SAMtools/tests/index_bams.nf
similarity index 100%
rename from src/docker_modules/SAMtools/tests/index_bams.nf
rename to src/nf_modules/SAMtools/tests/index_bams.nf
diff --git a/src/docker_modules/SAMtools/tests/sort_bams.nf b/src/nf_modules/SAMtools/tests/sort_bams.nf
similarity index 100%
rename from src/docker_modules/SAMtools/tests/sort_bams.nf
rename to src/nf_modules/SAMtools/tests/sort_bams.nf
diff --git a/src/docker_modules/SAMtools/tests/split_bams.nf b/src/nf_modules/SAMtools/tests/split_bams.nf
similarity index 100%
rename from src/docker_modules/SAMtools/tests/split_bams.nf
rename to src/nf_modules/SAMtools/tests/split_bams.nf
diff --git a/src/docker_modules/UrQt/tests/trimming_paired.nf b/src/nf_modules/UrQt/tests/trimming_paired.nf
similarity index 100%
rename from src/docker_modules/UrQt/tests/trimming_paired.nf
rename to src/nf_modules/UrQt/tests/trimming_paired.nf
diff --git a/src/docker_modules/UrQt/tests/trimming_single.nf b/src/nf_modules/UrQt/tests/trimming_single.nf
similarity index 100%
rename from src/docker_modules/UrQt/tests/trimming_single.nf
rename to src/nf_modules/UrQt/tests/trimming_single.nf
diff --git a/src/docker_modules/UrQt/urqt.config b/src/nf_modules/UrQt/urqt.config
similarity index 100%
rename from src/docker_modules/UrQt/urqt.config
rename to src/nf_modules/UrQt/urqt.config
diff --git a/src/docker_modules/UrQt/urqt.nf b/src/nf_modules/UrQt/urqt.nf
similarity index 100%
rename from src/docker_modules/UrQt/urqt.nf
rename to src/nf_modules/UrQt/urqt.nf
diff --git a/src/docker_modules/cutadapt/cutadapt.config b/src/nf_modules/cutadapt/cutadapt.config
similarity index 100%
rename from src/docker_modules/cutadapt/cutadapt.config
rename to src/nf_modules/cutadapt/cutadapt.config
diff --git a/src/docker_modules/cutadapt/cutadapt.nf b/src/nf_modules/cutadapt/cutadapt.nf
similarity index 100%
rename from src/docker_modules/cutadapt/cutadapt.nf
rename to src/nf_modules/cutadapt/cutadapt.nf
diff --git a/src/docker_modules/cutadapt/tests/adaptor_removal_paired.nf b/src/nf_modules/cutadapt/tests/adaptor_removal_paired.nf
similarity index 100%
rename from src/docker_modules/cutadapt/tests/adaptor_removal_paired.nf
rename to src/nf_modules/cutadapt/tests/adaptor_removal_paired.nf
diff --git a/src/docker_modules/cutadapt/tests/adaptor_removal_single.nf b/src/nf_modules/cutadapt/tests/adaptor_removal_single.nf
similarity index 100%
rename from src/docker_modules/cutadapt/tests/adaptor_removal_single.nf
rename to src/nf_modules/cutadapt/tests/adaptor_removal_single.nf
diff --git a/src/docker_modules/cutadapt/tests/trimming_paired.nf b/src/nf_modules/cutadapt/tests/trimming_paired.nf
similarity index 100%
rename from src/docker_modules/cutadapt/tests/trimming_paired.nf
rename to src/nf_modules/cutadapt/tests/trimming_paired.nf
diff --git a/src/docker_modules/cutadapt/tests/trimming_single.nf b/src/nf_modules/cutadapt/tests/trimming_single.nf
similarity index 100%
rename from src/docker_modules/cutadapt/tests/trimming_single.nf
rename to src/nf_modules/cutadapt/tests/trimming_single.nf
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