Unverified Commit f02083e7 authored by Chris Cheshire's avatar Chris Cheshire Committed by GitHub
Browse files

Merge pull request #131 from luslab/dev 

v2.0 updates
parents dbaad8c7 ca92a9b8

CHANGELOG.md

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@@ -98,7 +98,7 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi 
| ---------- | ----------- | ----------- |

| `samtools` | 1.14        | 1.15.1      |

| `bowtie2`  | 2.4.2       | 2.4.4       |

| `picard`   | 2.25.7      | 2.27.1      |

| `picard`   | 2.25.7      | 2.27.2      |



> **NB:** Dependency has been **updated** if both old and new version information is present.

> **NB:** Dependency has been **added** if just the new version information is present.

bin/check_samplesheet.py

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#!/usr/bin/env python



# This script is based on the example at: https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/design.csv





import os

import sys

import errno

conf/test.config

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@@ -20,7 +20,7 @@ params { 
    max_time   = '6.h'



    // Input data

    input = 'https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-small.csv'

    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-small.csv'



    // Genome references

    fasta              = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz'

conf/test_fasta_only.config

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@@ -8,7 +8,7 @@ params { 
    max_time   = 6.h



    // Input data

    input = 'https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-small.csv'

    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-small.csv'



    // Genome references

    fasta              = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz'

conf/test_full.config

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@@ -15,7 +15,7 @@ params { 
    config_profile_description = 'Full test dataset to check pipeline function'



    genome = 'GRCh38'

    input = 'https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-all.csv'

    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-all.csv'



    minimum_alignment_q_score = 10

}

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