13 |
14 | 
15 |
16 |
54 |
55 | <% out << summary.collect{ k,v -> "
58 |
59 |
63 |
64 |
65 |
66 |
--------------------------------------------------------------------------------
/CODE_OF_CONDUCT.md:
--------------------------------------------------------------------------------
1 | # Contributor Covenant Code of Conduct
2 |
3 | ## Our Pledge
4 |
5 | In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
6 |
7 | ## Our Standards
8 |
9 | Examples of behavior that contributes to creating a positive environment include:
10 |
11 | * Using welcoming and inclusive language
12 | * Being respectful of differing viewpoints and experiences
13 | * Gracefully accepting constructive criticism
14 | * Focusing on what is best for the community
15 | * Showing empathy towards other community members
16 |
17 | Examples of unacceptable behavior by participants include:
18 |
19 | * The use of sexualized language or imagery and unwelcome sexual attention or advances
20 | * Trolling, insulting/derogatory comments, and personal or political attacks
21 | * Public or private harassment
22 | * Publishing others' private information, such as a physical or electronic address, without explicit permission
23 | * Other conduct which could reasonably be considered inappropriate in a professional setting
24 |
25 | ## Our Responsibilities
26 |
27 | Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
28 |
29 | Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
30 |
31 | ## Scope
32 |
33 | This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
34 |
35 | ## Enforcement
36 |
37 | Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team on [Slack](https://nf-co.re/join/slack/). The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
38 |
39 | Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
40 |
41 | ## Attribution
42 |
43 | This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
44 |
45 | [homepage]: http://contributor-covenant.org
46 | [version]: http://contributor-covenant.org/version/1/4/
47 |
--------------------------------------------------------------------------------
/bin/scrape_software_versions.py:
--------------------------------------------------------------------------------
1 | #!/usr/bin/env python
2 | from __future__ import print_function
3 | from collections import OrderedDict
4 | import re
5 |
6 | regexes = {
7 | 'nf-core/rnaseq': ['v_ngi_rnaseq.txt', r"(\S+)"],
8 | 'Nextflow': ['v_nextflow.txt', r"(\S+)"],
9 | 'FastQC': ['v_fastqc.txt', r"FastQC v(\S+)"],
10 | 'Cutadapt': ['v_cutadapt.txt', r"(\S+)"],
11 | 'Trim Galore!': ['v_trim_galore.txt', r"version (\S+)"],
12 | 'SortMeRNA': ['v_sortmerna.txt', r"SortMeRNA version (\S+),"],
13 | 'STAR': ['v_star.txt', r"(\S+)"],
14 | 'HISAT2': ['v_hisat2.txt', r"version (\S+)"],
15 | 'Picard MarkDuplicates': ['v_markduplicates.txt', r"([\d\.]+)-SNAPSHOT"],
16 | 'Samtools': ['v_samtools.txt', r"samtools (\S+)"],
17 | 'featureCounts': ['v_featurecounts.txt', r"featureCounts v(\S+)"],
18 | 'Salmon': ['v_salmon.txt', r"salmon (\S+)"],
19 | 'deepTools': ['v_deeptools.txt', r"bamCoverage (\S+)"],
20 | 'StringTie': ['v_stringtie.txt', r"(\S+)"],
21 | 'Preseq': ['v_preseq.txt', r"Version: (\S+)"],
22 | 'RSeQC': ['v_rseqc.txt', r"read_duplication.py ([\d\.]+)"],
23 | 'Qualimap': ['v_qualimap.txt', r"QualiMap v(\S+)"],
24 | 'dupRadar': ['v_dupRadar.txt', r"(\S+)"],
25 | 'edgeR': ['v_edgeR.txt', r"(\S+)"],
26 | 'MultiQC': ['v_multiqc.txt', r"multiqc, version (\S+)"],
27 | }
28 | results = OrderedDict()
29 | results['nf-core/rnaseq'] = 'N/A'
30 | results['Nextflow'] = 'N/A'
31 | results['FastQC'] = 'N/A'
32 | results['Cutadapt'] = 'N/A'
33 | results['Trim Galore!'] = 'N/A'
34 | results['SortMeRNA'] = 'N/A'
35 | results['STAR'] = False
36 | results['HISAT2'] = False
37 | results['Picard MarkDuplicates'] = 'N/A'
38 | results['Samtools'] = 'N/A'
39 | results['featureCounts'] = 'N/A'
40 | results['Salmon'] = 'N/A'
41 | results['StringTie'] = 'N/A'
42 | results['Preseq'] = 'N/A'
43 | results['deepTools'] = 'N/A'
44 | results['RSeQC'] = 'N/A'
45 | results['dupRadar'] = 'N/A'
46 | results['edgeR'] = 'N/A'
47 | results['Qualimap'] = 'N/A'
48 | results['MultiQC'] = 'N/A'
49 |
50 | # Search each file using its regex
51 | for k, v in regexes.items():
52 | try:
53 | with open(v[0]) as x:
54 | versions = x.read()
55 | match = re.search(v[1], versions)
56 | if match:
57 | results[k] = "v{}".format(match.group(1))
58 | except IOError:
59 | results[k] = False
60 |
61 | # Strip STAR or HiSAT2
62 | for k in results:
63 | if not results[k]:
64 | del(results[k])
65 |
66 | # Dump to YAML
67 | print ('''
68 | id: 'software_versions'
69 | section_name: 'nf-core/rnaseq Software Versions'
70 | section_href: 'https://github.com/nf-core/rnaseq'
71 | plot_type: 'html'
72 | description: 'are collected at run time from the software output.'
73 | data: |
74 | nf-core/rnaseq v${version}
17 |Run Name: $runName
18 | 19 | <% if (!success){ 20 | out << """ 21 |
22 |
27 | """
28 | } else if(skipped_poor_alignment.size() > 0) {
29 | out << """
30 | nf-core/rnaseq execution completed unsuccessfully!
23 |The exit status of the task that caused the workflow execution to fail was: $exitStatus.
The full error message was:
25 |${errorReport}
26 |
31 |
38 | """
39 | } else {
40 | out << """
41 | nf-core/rnaseq execution completed with warnings!
32 |The pipeline finished successfully, but the following samples were skipped due to very low alignment (< 5%):
33 |-
34 |
${skipped_poor_alignment.join('')}
35 |
37 |
42 | nf-core/rnaseq execution completed successfully!
43 |
44 | """
45 | }
46 | %>
47 |
48 | The workflow was completed at $dateComplete (duration: $duration)
49 |The command used to launch the workflow was as follows:
50 |$commandLine51 | 52 |
Pipeline Configuration:
53 || $k | $v |
|---|
nf-core/rnaseq
60 | 61 | 62 |-
75 | ''')
76 | for k,v in results.items():
77 | print("
- {}
- {} ".format(k,v)) 78 | print ("