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LBMC
Hub
hic
Commits
7996e983
Commit
7996e983
authored
2 years ago
by
nservant
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[TEST] move samplesheet to assets for test
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4edc94cb
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README.md
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README.md
assets/samplesheet.csv
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assets/samplesheet.csv
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README.md
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View file @
7996e983
...
@@ -25,7 +25,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
...
@@ -25,7 +25,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
1.
Read QC (
[
`FastQC`
](
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
)
)
1.
Read QC (
[
`FastQC`
](
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
)
)
2.
Hi-C data processing
2.
Hi-C data processing
1.
with
[
`HiC-Pro`
](
https://github.com/nservant/HiC-Pro
)
1.
[
`HiC-Pro`
](
https://github.com/nservant/HiC-Pro
)
1.
Mapping using a two steps strategy to rescue reads spanning the ligation
1.
Mapping using a two steps strategy to rescue reads spanning the ligation
sites (
[
`bowtie2`
](
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
)
)
sites (
[
`bowtie2`
](
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
)
)
2.
Detection of valid interaction products
2.
Detection of valid interaction products
...
...
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assets/samplesheet.csv
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7996e983
sample,fastq_1,fastq_2
sample,fastq_1,fastq_2
SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz
SRR4292758,https://github.com/nf-core/test-datasets/raw/hic/data/SRR4292758_00_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/hic/data/SRR4292758_00_R2.fastq.gz
SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,
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