Ver2rc

.devcontainer/devcontainer.json

@@ -2,6 +2,7 @@
     "name": "nfcore",
     "image": "nfcore/gitpod:latest",
     "remoteUser": "gitpod",
+    "runArgs": ["--privileged"],
 
     // Configure tool-specific properties.
     "customizations": {

.github/CONTRIBUTING.md

@@ -9,7 +9,9 @@ Please use the pre-filled template to save time.
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
-> If you need help using or modifying nf-core/hicar then the best place to ask is on the nf-core Slack [#hicar](https://nfcore.slack.com/channels/hicar) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::info
+If you need help using or modifying nf-core/hicar then the best place to ask is on the nf-core Slack [#hicar](https://nfcore.slack.com/channels/hicar) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::
 
 ## Contribution workflow
 

.github/workflows/ci.yml

@@ -43,6 +43,11 @@ jobs:
           - "--method HiChIP --anchor_peaks 'https://raw.githubusercontent.com/aryeelab/hichipper/master/tests/chipseq/GM12878_SMC3_ChIPSeq_chr22.narrowPeak'"
 
     steps:
+      - name: Free Disk Space (Ubuntu)
+        uses: jlumbroso/free-disk-space@main
+        with:
+          tool-cache: true
+
       - name: Check out pipeline code
         uses: actions/checkout@v3
 

.github/workflows/linting.yml

@@ -78,7 +78,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.8"
+          python-version: "3.11"
           architecture: "x64"
 
       - name: Install dependencies

.github/workflows/release-announcments.yml

@@ -0,0 +1,68 @@
+name: release-announcements
+# Automatic release toot and tweet anouncements
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  toot:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: rzr/fediverse-action@master
+        with:
+          access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
+          host: "mstdn.science" # custom host if not "mastodon.social" (default)
+          # GitHub event payload
+          # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
+          message: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+
+  send-tweet:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: pip install tweepy==4.14.0
+      - name: Send tweet
+        shell: python
+        run: |
+          import os
+          import tweepy
+
+          client = tweepy.Client(
+              access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
+              access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
+              consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
+              consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
+          )
+          tweet = os.getenv("TWEET")
+          client.create_tweet(text=tweet)
+        env:
+          TWEET: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+          TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
+          TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
+          TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
+          TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}
+
+  bsky-post:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: zentered/bluesky-post-action@v0.0.2
+        with:
+          post: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+        env:
+          BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }}
+          BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }}
+          #

CHANGELOG.md

@@ -3,12 +3,11 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v2.0.0 - [07/13/2023]
+## v2.0.0dev - [10/10/2023]
 
-- [[#89](https://github.com/nf-core/hicar/pull/89)] - update to nf-core-template-2.9
-- [[#90](https://github.com/nf-core/hicar/pull/90)] - remove the output folder setting from config files
-- [replace the dots](https://github.com/nf-core/hicar/pull/89#issue-1797065776) by '\_' in the samples group
-- add [support for MseI](https://github.com/jianhong/hicar/commit/64bfcecab9870100d56631ffc31ff0ed471e1255).
+- update to nf-core-template-2.7.2
+- replace the dots by '\_' in the samples name
+- add support for MseI.
 - add TAD, AB compartments, APA analysis (see available tools in usage documentation)
 - add additional methods for interaction caller
 - adjust default resource requirement
@@ -20,13 +19,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - removed local_modules tests
 - add scale factor to atac reads coverage calculation
 - change the circos plot style
-- update reads_summary table to include unmapped/multiple mapped info
+- update reads_summary table to include unmapped/multiple mapped, same fragement info
+- change the TSSEscore from 1K upstream/downstream to 2K range.
 - add the possibility to subsample to balance the input reads
 - add parameter to let user input the 5 end sequence to cutadapt step
 - change the cutadapt error tolerance from 0 to 0.15
-- changes in hipeak caller:
-  - add filter condition for lowest count number as 1.
-  - change the cutoff value for hipeak type assignment step from 12 to 3.
+- change the default cutadapt_action from none to trim
+- add 3' trim to remove the second enzyme site if it appeared in after 50 base.
+- export parameter for prepare trans counts for MAPS
+- add parameter to select pairtools parse or parse2
+- export parameter for pairtools parse and parse2
+- add function to detect the contamination by karken2
 - fix multiple bugs:
   - the sorting method for huge bed file;
   - the post count for hipeak when there is empty Interactions;
@@ -36,7 +39,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - fix the chromosome style for homer TFEA analysis and annotation by ChIPpeakAnno;
   - fix the duplicated imported modules;
   - fix multiple typos.
-  - use local SAMTOOLS_SORT module;
 
 ## v1.0.0 - [05/03/2022]
 

CITATIONS.md

@@ -50,7 +50,7 @@
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
-  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
+  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
 - [GenMap](https://pubmed.ncbi.nlm.nih.gov/32246826/)
 
@@ -76,6 +76,10 @@
 
   > Durand NC, Shamim MS, Machol I, Rao SS, Huntley MH, Lander ES, Aiden EL. Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. Cell Syst. 2016 Jul;3(1):95-8. doi: 10.1016/j.cels.2016.07.002. PMID: 27467249; PMCID: PMC5846465.
 
+- [Kraken 2](https://ccb.jhu.edu/software/kraken2/)
+
+  > Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol. 2019 Nov 28;20(1):257. doi: 10.1186/s13059-019-1891-0. PMID: 31779668; PMCID: PMC6883579.
+
 - [MACS2](https://www.ncbi.nlm.nih.gov/pubmed/18798982/)
 
   > Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. doi: 10.1186/gb-2008-9-9-r137. Epub 2008 Sep 17. PubMed PMID: 18798982; PubMed Central PMCID: PMC2592715.