Merge pull request #51 from drpatelh/master

Test latest FastQC implementation
2025-01-18 02:46:13 -05:00 · 2020-08-05 16:10:41 +01:00 · 2020-08-05 16:10:41 +01:00 · 2b6a68260b
commit 2b6a68260b
parent 88eac382be c08e6959a5
178 changed files with 84 additions and 37 deletions
--- a/deprecated/bedtools/complement/Dockerfile
+++ b/deprecated/bedtools/complement/Dockerfile
--- a/deprecated/bedtools/complement/environment.yml
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--- a/deprecated/bedtools/complement/main.nf
+++ b/deprecated/bedtools/complement/main.nf
--- a/deprecated/bedtools/complement/meta.yml
+++ b/deprecated/bedtools/complement/meta.yml
--- a/deprecated/bedtools/complement/test/input_data/A.bed
+++ b/deprecated/bedtools/complement/test/input_data/A.bed
--- a/deprecated/bedtools/complement/test/input_data/genome.sizes
+++ b/deprecated/bedtools/complement/test/input_data/genome.sizes
--- a/deprecated/bedtools/complement/test/main.nf
+++ b/deprecated/bedtools/complement/test/main.nf
--- a/deprecated/bedtools/genomecov/Dockerfile
+++ b/deprecated/bedtools/genomecov/Dockerfile
--- a/deprecated/bedtools/genomecov/environment.yml
+++ b/deprecated/bedtools/genomecov/environment.yml
--- a/deprecated/bedtools/genomecov/main.nf
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--- a/deprecated/bedtools/genomecov/meta.yml
+++ b/deprecated/bedtools/genomecov/meta.yml
--- a/deprecated/bedtools/genomecov/test/input_data/JK2067_downsampled_s0.1.bam
+++ b/deprecated/bedtools/genomecov/test/input_data/JK2067_downsampled_s0.1.bam
--- a/deprecated/bedtools/genomecov/test/input_data/genome.sizes
+++ b/deprecated/bedtools/genomecov/test/input_data/genome.sizes
--- a/deprecated/bedtools/genomecov/test/main.nf
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--- a/deprecated/bedtools/intersect/Dockerfile
+++ b/deprecated/bedtools/intersect/Dockerfile
--- a/deprecated/bedtools/intersect/environment.yml
+++ b/deprecated/bedtools/intersect/environment.yml
--- a/deprecated/bedtools/intersect/main.nf
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--- a/deprecated/bedtools/intersect/meta.yml
+++ b/deprecated/bedtools/intersect/meta.yml
--- a/deprecated/bedtools/intersect/test/input_data/A.bed
+++ b/deprecated/bedtools/intersect/test/input_data/A.bed
--- a/deprecated/bedtools/intersect/test/input_data/B.bed
+++ b/deprecated/bedtools/intersect/test/input_data/B.bed
--- a/deprecated/bedtools/intersect/test/main.nf
+++ b/deprecated/bedtools/intersect/test/main.nf
--- a/deprecated/bedtools/merge/Dockerfile
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--- a/deprecated/bedtools/merge/environment.yml
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--- a/deprecated/bedtools/merge/main.nf
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--- a/deprecated/bedtools/merge/meta.yml
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--- a/deprecated/bedtools/merge/test/input_data/A.bed
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--- a/deprecated/bedtools/merge/test/input_data/JK2067_downsampled_s0.1.bam
+++ b/deprecated/bedtools/merge/test/input_data/JK2067_downsampled_s0.1.bam
--- a/deprecated/bedtools/merge/test/main.nf
+++ b/deprecated/bedtools/merge/test/main.nf
--- a/deprecated/bedtools/merge/test/nextflow.config
+++ b/deprecated/bedtools/merge/test/nextflow.config
--- a/deprecated/bedtools/sort/environment.yml
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--- a/deprecated/bedtools/sort/main.nf
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--- a/deprecated/bedtools/sort/meta.yml
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--- a/deprecated/bedtools/sort/test/input_data/A.bed
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--- a/deprecated/bedtools/sort/test/main.nf
+++ b/deprecated/bedtools/sort/test/main.nf
--- a/deprecated/bowtie2/main.nf
+++ b/deprecated/bowtie2/main.nf
--- a/deprecated/bowtie2/meta.yml
+++ b/deprecated/bowtie2/meta.yml
--- a/deprecated/bowtie2/test/indices/E_coli/E_coli.1.bt2
+++ b/deprecated/bowtie2/test/indices/E_coli/E_coli.1.bt2
--- a/deprecated/bowtie2/test/indices/E_coli/E_coli.2.bt2
+++ b/deprecated/bowtie2/test/indices/E_coli/E_coli.2.bt2
--- a/deprecated/bowtie2/test/indices/E_coli/E_coli.3.bt2
+++ b/deprecated/bowtie2/test/indices/E_coli/E_coli.3.bt2
--- a/deprecated/bowtie2/test/indices/E_coli/E_coli.4.bt2
+++ b/deprecated/bowtie2/test/indices/E_coli/E_coli.4.bt2
--- a/deprecated/bowtie2/test/indices/E_coli/E_coli.rev.1.bt2
+++ b/deprecated/bowtie2/test/indices/E_coli/E_coli.rev.1.bt2
--- a/deprecated/bowtie2/test/indices/E_coli/E_coli.rev.2.bt2
+++ b/deprecated/bowtie2/test/indices/E_coli/E_coli.rev.2.bt2
--- a/deprecated/bowtie2/test/indices/E_coli/NC_010473.fa
+++ b/deprecated/bowtie2/test/indices/E_coli/NC_010473.fa
--- a/deprecated/bowtie2/test/input/Ecoli_DNA_R1.fastq.gz
+++ b/deprecated/bowtie2/test/input/Ecoli_DNA_R1.fastq.gz
--- a/deprecated/bowtie2/test/input/Ecoli_DNA_R2.fastq.gz
+++ b/deprecated/bowtie2/test/input/Ecoli_DNA_R2.fastq.gz
--- a/deprecated/bowtie2/test/input/test_R1_val_1.fq.gz
+++ b/deprecated/bowtie2/test/input/test_R1_val_1.fq.gz
--- a/deprecated/bowtie2/test/input/test_R2_val_2.fq.gz
+++ b/deprecated/bowtie2/test/input/test_R2_val_2.fq.gz
--- a/deprecated/bowtie2/test/main.nf
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--- a/deprecated/bowtie2/test/nextflow.config
+++ b/deprecated/bowtie2/test/nextflow.config
--- a/deprecated/bowtie2/test/output/Ecoli_DNA_R_E_coli_bowtie2.bam
+++ b/deprecated/bowtie2/test/output/Ecoli_DNA_R_E_coli_bowtie2.bam
--- a/deprecated/bowtie2/test/output/Ecoli_DNA_R_E_coli_bowtie2_stats.txt
+++ b/deprecated/bowtie2/test/output/Ecoli_DNA_R_E_coli_bowtie2_stats.txt
--- a/deprecated/bowtie2/test/output/test_GRCm38_bowtie2.bam
+++ b/deprecated/bowtie2/test/output/test_GRCm38_bowtie2.bam
--- a/deprecated/bowtie2/test/output/test_GRCm38_bowtie2_stats.txt
+++ b/deprecated/bowtie2/test/output/test_GRCm38_bowtie2_stats.txt
--- a/deprecated/bwa-mem2/index/main.nf
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--- a/deprecated/bwa-mem2/index/meta.yml
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--- a/deprecated/bwa-mem2/index/test/main.nf
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--- a/deprecated/bwa-mem2/index/test/nextflow.config
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--- a/deprecated/bwa/index/main.nf
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--- a/deprecated/bwa/index/meta.yml
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--- a/deprecated/bwa/index/test/main.nf
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--- a/deprecated/bwa/index/test/nextflow.config
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--- a/deprecated/bwa/mem/Dockerfile
+++ b/deprecated/bwa/mem/Dockerfile
--- a/deprecated/bwa/mem/environment.yml
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--- a/deprecated/bwa/mem/main.nf
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--- a/deprecated/bwa/mem/meta.yml
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--- a/deprecated/bwa/mem/test/main.nf
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--- a/deprecated/bwa/mem/test/nextflow.config
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--- a/deprecated/cutadapt/main.nf
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--- a/deprecated/cutadapt/meta.yml
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--- a/deprecated/cutadapt/test/main.nf
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--- a/deprecated/cutadapt/test/nextflow.config
+++ b/deprecated/cutadapt/test/nextflow.config
--- a/deprecated/fastq_screen/main.nf
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--- a/deprecated/fastq_screen/meta.yml
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--- a/deprecated/fastq_screen/test/input/test_R1.fastq.gz
+++ b/deprecated/fastq_screen/test/input/test_R1.fastq.gz
--- a/deprecated/fastq_screen/test/input/test_R1_val_1.fq.gz
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--- a/deprecated/fastq_screen/test/input/test_R2.fastq.gz
+++ b/deprecated/fastq_screen/test/input/test_R2.fastq.gz
--- a/deprecated/fastq_screen/test/input/test_R2_val_2.fq.gz
+++ b/deprecated/fastq_screen/test/input/test_R2_val_2.fq.gz
--- a/deprecated/fastq_screen/test/input/test_single_end.fastq.gz
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--- a/deprecated/fastq_screen/test/main.nf
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--- a/deprecated/fastq_screen/test/nextflow.config
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--- a/deprecated/fastq_screen/test/output/test_R1_screen.txt
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--- a/deprecated/gatk/dict/main.nf
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--- a/deprecated/gatk/dict/meta.yml
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--- a/deprecated/gatk/dict/test/main.nf
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--- a/software/htslib/tabix/test/nextflow.config
+++ b/software/htslib/tabix/test/nextflow.config
--- a/deprecated/hisat2/main.nf
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--- a/deprecated/hisat2/meta.yml
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--- a/deprecated/hisat2/test/indices/E_coli/E_coli.1.ht2
+++ b/deprecated/hisat2/test/indices/E_coli/E_coli.1.ht2
--- a/deprecated/hisat2/test/indices/E_coli/E_coli.2.ht2
+++ b/deprecated/hisat2/test/indices/E_coli/E_coli.2.ht2
--- a/deprecated/hisat2/test/indices/E_coli/E_coli.3.ht2
+++ b/deprecated/hisat2/test/indices/E_coli/E_coli.3.ht2
--- a/deprecated/hisat2/test/indices/E_coli/E_coli.4.ht2
+++ b/deprecated/hisat2/test/indices/E_coli/E_coli.4.ht2
--- a/deprecated/hisat2/test/indices/E_coli/E_coli.5.ht2
+++ b/deprecated/hisat2/test/indices/E_coli/E_coli.5.ht2
--- a/deprecated/hisat2/test/indices/E_coli/E_coli.6.ht2
+++ b/deprecated/hisat2/test/indices/E_coli/E_coli.6.ht2
--- a/deprecated/hisat2/test/indices/E_coli/E_coli.7.ht2
+++ b/deprecated/hisat2/test/indices/E_coli/E_coli.7.ht2
--- a/deprecated/hisat2/test/indices/E_coli/E_coli.8.ht2
+++ b/deprecated/hisat2/test/indices/E_coli/E_coli.8.ht2
--- a/deprecated/hisat2/test/indices/E_coli/NC_010473.fa
+++ b/deprecated/hisat2/test/indices/E_coli/NC_010473.fa
--- a/deprecated/hisat2/test/input/Ecoli_DNA_R1.fastq.gz
+++ b/deprecated/hisat2/test/input/Ecoli_DNA_R1.fastq.gz
--- a/deprecated/hisat2/test/input/Ecoli_DNA_R2.fastq.gz
+++ b/deprecated/hisat2/test/input/Ecoli_DNA_R2.fastq.gz
--- a/deprecated/hisat2/test/main.nf
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--- a/deprecated/hisat2/test/nextflow.config
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--- a/Show more
+++ b/Show more