Release 1.0.0 (dev branch)

.devcontainer/devcontainer.json

@@ -1,20 +1,20 @@
 {
     "name": "nfcore",
-    "image": "nfcore/gitpod:latest",
-    "remoteUser": "gitpod",
-    "runArgs": ["--privileged"],
+    "image": "nfcore/devcontainer:latest",
 
-    // Configure tool-specific properties.
-    "customizations": {
-        // Configure properties specific to VS Code.
-        "vscode": {
-            // Set *default* container specific settings.json values on container create.
-            "settings": {
-                "python.defaultInterpreterPath": "/opt/conda/bin/python"
-            },
+    "remoteUser": "root",
+    "privileged": true,
 
-            // Add the IDs of extensions you want installed when the container is created.
-            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
-        }
+    "remoteEnv": {
+        // Workspace path on the host for mounting with docker-outside-of-docker
+        "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
+    },
+
+    "onCreateCommand": "./.devcontainer/setup.sh",
+
+    "hostRequirements": {
+        "cpus": 4,
+        "memory": "16gb",
+        "storage": "32gb"
     }
 }

.devcontainer/setup.sh

@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+
+# Customise the terminal command prompt
+echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc
+echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc
+export PROMPT_DIRTRIM=2
+export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
+
+# Update Nextflow
+nextflow self-update
+
+# Update welcome message
+echo "Welcome to the nf-core/nextbigthing devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt

.github/workflows/linting.yml

@@ -11,12 +11,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
-      - name: Set up Python 3.13
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - name: Set up Python 3.14
+        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -28,14 +28,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
           architecture: "x64"
 
       - name: read .nf-core.yml
@@ -71,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: linting-logs
           path: |

.github/workflows/linting_comment.yml

@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2
+        uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}

.github/workflows/nf-test.yml

@@ -50,7 +50,7 @@ jobs:
         env:
           NFT_VER: ${{ env.NFT_VER }}
         with:
-          max_shards: 7
+          max_shards: 15
 
       - name: debug
         run: |
@@ -68,7 +68,7 @@ jobs:
       fail-fast: false
       matrix:
         shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }}
-        profile: [conda, docker, singularity]
+        profile: [docker, singularity]
         isMain:
           - ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
         # Exclude conda and singularity on dev
@@ -79,7 +79,6 @@ jobs:
             profile: "singularity"
         NXF_VER:
           - "24.10.5"
-          - "latest-everything"
     env:
       NXF_ANSI_LOG: false
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
@@ -99,7 +98,17 @@ jobs:
           profile: ${{ matrix.profile }}
           shard: ${{ matrix.shard }}
           total_shards: ${{ env.TOTAL_SHARDS }}
-
+      - name: list contents
+        run: ls -R "${{ env.NFT_WORKDIR }}"
+      - name: list funcprofilercontents
+        run: ls -R /home/runner/_work/funcprofiler/funcprofiler/
+      - name: Upload artifact
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v7
+        with:
+          name: my-artifact-${{ matrix.profile }}-${{ matrix.NXF_VER }}-${{ matrix.shard }}
+          path: /home/runner/_work/funcprofiler/funcprofiler/
+          retention-days: 2
       - name: Report test status
         if: ${{ always() }}
         run: |
@@ -118,7 +127,7 @@ jobs:
   confirm-pass:
     needs: [nf-test]
     if: always()
-    runs-on:  # use self-hosted runners
+    runs-on: # use self-hosted runners
       - runs-on=${{ github.run_id }}-confirm-pass
       - runner=2cpu-linux-x64
     steps:

.gitignore

@@ -7,3 +7,10 @@ testing/
 testing*
 *.pyc
 null/
+*~
+.nf-test/
+.nf-test.log
+dontcommit
+tmp/
+.data/
+*.code-workspace

.nf-core.yml

@@ -1,8 +1,11 @@
 repository_type: pipeline
 
-nf_core_version: 3.3.2
+nf_core_version: 3.5.2
 
-lint: {}
+lint:
+  files_unchanged:
+    - assets/nf-core-funcprofiler_logo_light.png
+    - .github/PULL_REQUEST_TEMPLATE.md
 
 template:
   org: nf-core

.prettierignore

@@ -10,4 +10,7 @@ testing/
 testing*
 *.pyc
 bin/
+.nf-test/
 ro-crate-metadata.json
+modules/nf-core/
+subworkflows/nf-core/

CITATIONS.md

@@ -10,6 +10,10 @@
 
 ## Pipeline tools
 
+- [DIAMOND](https://github.com/bbuchfink/diamond/)
+
+> Buchfink B, Reuter K, Drost HG. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat Methods. 2021 Apr;18(4):366-368. doi: 10.1038/s41592-021-01101-x. PubMed PMID: 33828273.
+
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
 > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

README.md

@@ -20,48 +20,63 @@
 
 ## Introduction
 
-**nf-core/funcprofiler** is a bioinformatics pipeline that ...
-
-<!-- TODO nf-core:
-   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
-   major pipeline sections and the types of output it produces. You're giving an overview to someone new
-   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction
--->
-
 <!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
      workflows use the "tube map" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->
-<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+
+**nf-core/funcprofiler** is a bioinformatics pipeline for read-based functional profiling of microbiome sequencing data. It accepts short-read (Illumina) and long-read (Oxford Nanopore) FASTQ files and runs one or more functional profilers against user-supplied databases, producing gene family abundances, pathway abundances, pathway coverages, and antimicrobial resistance profiles.
+
+### Pipeline Summary
+
+![](./assets/pipeline_light.svg)
+
+Supported profilers:
+
+1. [**HUMANn v3**](https://huttenhower.sph.harvard.edu/humann/) — functional profiling via MetaPhlAn + HUMANn 3 (`--run_humann_v3`)
+2. [**HUMANn v4**](https://huttenhower.sph.harvard.edu/humann/) — functional profiling via MetaPhlAn + HUMANn 4 (`--run_humann_v4`)
+3. [**FMH FunProfiler**](https://github.com/dib-lab/fmh_funprofiler) — sketch-based functional profiling (`--run_fmhfunprofiler`)
+4. [**RGI**](https://github.com/arpcard/rgi) — antimicrobial resistance gene identification (`--run_rgi`, available)
+5. [**mifaser**](https://bromberglab.org/project/mifaser/) — functional profiling via mifaser (`--run_mifaser`, available)
+6. [**DIAMOND**](https://github.com/bbuchfink/diamond) — alignment with DIAMOND blastx (`--run_diamond`, available)
+7. [**eggNOG-mapper**](https://academic.oup.com/mbe/article/38/12/5825/6379734) — functional annotation, orthology assignments and domain prediction (`--run_eggnogmapper`, available)
 
 ## Usage
 
 > [!NOTE]
 > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
 
-<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
-     Explain what rows and columns represent. For instance (please edit as appropriate):
-
-First, prepare a samplesheet with your input data that looks as follows:
+First, prepare a samplesheet with your input data:
 
 `samplesheet.csv`:
 
 ```csv
-sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
+sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
+SAMPLE1,RUN1,ILLUMINA,/path/to/sample1_R1.fastq.gz,/path/to/sample1_R2.fastq.gz,
+SAMPLE2,RUN1,OXFORD_NANOPORE,/path/to/sample2.fastq.gz,,
 ```
 
-Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
+Each row represents a sequencing run. Multiple rows with the same `sample` and different `run_accession` values will be merged before profiling.
 
--->
+Then prepare a databases sheet — see [docs/usage.md](docs/usage.md) for the full format. Here is an abbreviated example for running HUMANn (which requires 4 databases):
 
-Now, you can run the pipeline using:
+`databases.csv`
+
+```csv
+tool,db_name,db_entity,db_params,db_type,db_path
+humann_v3,uniref90_v3,humann_metaphlan,,,/data/databases/metaphlan_db
+humann_v3,uniref90_v3,humann_nucleotide,,,/data/databases/chocophlan
+humann_v3,uniref90_v3,humann_protein,,,/data/databases/uniref90_diamond
+humann_v3,uniref90_v3,humann_utility,,,/data/databases/utility_mapping
+```
 
-<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
+Now, you can run the pipeline using:
 
 ```bash
 nextflow run nf-core/funcprofiler \
    -profile <docker/singularity/.../institute> \
    --input samplesheet.csv \
-   --outdir <OUTDIR>
+   --outdir <OUTDIR> \
+   --databases databases.csv \
+   --run_humann_v3
 ```
 
 > [!WARNING]
@@ -77,7 +92,7 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/funcprofiler was originally written by Nick Waters.
+nf-core/funcprofiler was written by Nick Waters, Vini Salazar, Yixuan Yang, Mirae Baichoo.
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 

assets/nf-metro_command.sh

@@ -0,0 +1,2 @@
+nf-metro render pipeline.mmd -o pipeline_light.svg --logo nf-core-funcprofiler_logo_light.png --theme light --animate
+nf-metro render pipeline.mmd -o pipeline_nf-core.svg --logo nf-core-funcprofiler_logo_light.png --theme nfcore --animate

assets/pipeline.mmd

@@ -0,0 +1,79 @@
+graph LR
+    %%metro line: qc | Preprocessing & QC | #4CAF50
+    %%metro line: concat | Merge & Concat | #2196F3
+    %%metro line: humann3 | HUMAnN v3 | #FF9800
+    %%metro line: humann4 | HUMAnN v4 | #FF5722
+    %%metro line: fmhfunprofiler | FMH FunProfiler | #E91E63
+    %%metro line: rgi | RGI | #CDDC39
+    %%metro line: mifaser | mifaser | #00BCD4
+    %%metro line: diamond | DIAMOND | #9C27B0
+    %%metro line: eggnog | eggNOG-mapper | #3F51B5
+    %%metro line: multiqc | Reporting | #795548
+    %%metro line: db | Database Prep | #607D8B
+
+    subgraph input[Input]
+        input_short([Short Read\nFASTQ])
+        input_dbs([Input Databases])
+        sr_qc(Preprocess)
+        merge(MERGE_RUNS)
+    end
+
+    subgraph profiling[Functional Profiling]
+        humann3(HUMAnN v3)
+        humann4(HUMAnN v4)
+        fmhfunprofiler(FMH FunProfiler)
+        RGI(RGI)
+        mifaser(mifaser)
+        diamond(DIAMOND)
+        eggnog_mapper(eggNOG-mapper)
+    end
+
+    subgraph QC[Quality Check]
+        multiqc(MultiQC)
+    end
+
+    subgraph Output[Output]
+        output([Results Directory])
+    end
+
+    %% DB Prep
+    input_dbs -->|db| humann3
+    input_dbs -->|db| humann4
+    input_dbs -->|db| fmhfunprofiler
+    input_dbs -->|db| RGI
+    input_dbs -->|db| mifaser
+    input_dbs -->|db| diamond
+    input_dbs -->|db| eggnog_mapper
+
+    %% Preprocessing
+    input_short -->|qc| sr_qc
+    sr_qc -->|concat| merge
+
+    %% Profiling split
+    merge -->|humann3| humann3
+    merge -->|humann4| humann4
+    merge -->|fmhfunprofiler| fmhfunprofiler
+    merge -->|rgi| RGI
+    merge -->|mifaser| mifaser
+    merge -->|diamond| diamond
+    merge -->|eggnog| eggnog_mapper
+
+    %% Reporting
+    sr_qc -->|multiqc| multiqc
+    humann3 -->|multiqc| multiqc
+    humann4 -->|multiqc| multiqc
+    fmhfunprofiler -->|multiqc| multiqc
+    RGI -->|multiqc| multiqc
+    mifaser -->|multiqc| multiqc
+    diamond -->|multiqc| multiqc
+    eggnog_mapper -->|multiqc| multiqc
+
+    %% Output
+    multiqc -->|multiqc| output
+    humann3 -->|humann3| output
+    humann4 -->|humann4| output
+    fmhfunprofiler -->|fmhfunprofiler| output
+    RGI -->|rgi| output
+    mifaser -->|mifaser| output
+    diamond -->|diamond| output
+    eggnog_mapper -->|eggnog| output