fix bbmap version

clean configs

modify readme

.github/workflows/docker.yml

@@ -34,8 +34,8 @@ jobs:
           #   image: denglab/viroprofiler-bracken
           # - dockerfile: ./docker/viroprofiler-phamb/Dockerfile
           #   image: denglab/viroprofiler-phamb
-          - dockerfile: ./docker/viroprofiler-virsorter2/Dockerfile
-            image: denglab/viroprofiler-virsorter2
+          # - dockerfile: ./docker/viroprofiler-virsorter2/Dockerfile
+          #   image: denglab/viroprofiler-virsorter2
     permissions:
       contents: read
       packages: write

README.md

@@ -27,23 +27,33 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 
 ## Quick Start
 
-1. Install [Miniconda3](https://docs.conda.io/en/latest/miniconda.html).
+1. Install one of the supported container engines using **root** privileges:
 
-2. Install Nextflow and Singularity using conda:
+   - [Singularity](https://sylabs.io/guides/3.0/user-guide/quick_start.html#quick-installation-steps)
+   - [Charliecloud](https://hpc.github.io/charliecloud/install.html)
+   - [Docker](https://docs.docker.com/install/)
+   - [Podman](https://podman.io/getting-started/installation)
+   - [Shifter](https://github.com/NERSC/shifter)
+
+2. Install [Miniconda3](https://docs.conda.io/en/latest/miniconda.html).
+
+3. Install Nextflow using conda:
 
    ```bash
    # You may need to restart your terminal before running the following commands
-   conda install -c conda-forge -c bioconda nextflow singularity
+   conda install -c bioconda nextflow
    ```
 
-3. Download the pipeline and database.
+4. Download the pipeline and database.
 
    ```bash
    # setup database
    nextflow run deng-lab/viroprofiler -r main -profile singularity --mode "setup"
    ```
 
-4. Run the pipeline,
+   `-profile` specifies the container engine to use. You can use `singularity`, `charliecloud`, `docker`, `podman`, or `shifter`. You can also use `test` to run the pipeline with test data after setting up the database.
+
+5. Run the pipeline,
 
    ```bash
    # run test
@@ -53,7 +63,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
    nextflow run deng-lab/viroprofiler -r main -profile singularity --input samplesheet.csv
    ```
 
-5. Update the pipeline,
+6. Update the pipeline,
 
    ```bash
    nextflow pull deng-lab/viroprofiler

assets/samplesheet.csv

@@ -1,16 +1,6 @@
 sample,fastq_1,fastq_2
-HT01,https://raw.githubusercontent.com/rujinlong/test/main/data/HT01_R1.fq.gz,https://raw.githubusercontent.com/rujinlong/test/main/data/HT01_R2.fq.gz
 HT02,https://raw.githubusercontent.com/rujinlong/test/main/data/HT02_R1.fq.gz,https://raw.githubusercontent.com/rujinlong/test/main/data/HT02_R2.fq.gz
 HT04,https://raw.githubusercontent.com/rujinlong/test/main/data/HT04_R1.fq.gz,https://raw.githubusercontent.com/rujinlong/test/main/data/HT04_R2.fq.gz
-HT05,https://raw.githubusercontent.com/rujinlong/test/main/data/HT05_R1.fq.gz,https://raw.githubusercontent.com/rujinlong/test/main/data/HT05_R2.fq.gz
-HT23,https://raw.githubusercontent.com/rujinlong/test/main/data/HT23_R1.fq.gz,https://raw.githubusercontent.com/rujinlong/test/main/data/HT23_R2.fq.gz
-HT24,https://raw.githubusercontent.com/rujinlong/test/main/data/HT24_R1.fq.gz,https://raw.githubusercontent.com/rujinlong/test/main/data/HT24_R2.fq.gz
 UC20,https://raw.githubusercontent.com/rujinlong/test/main/data/UC20_R1.fq.gz,https://raw.githubusercontent.com/rujinlong/test/main/data/UC20_R2.fq.gz
 UC21,https://raw.githubusercontent.com/rujinlong/test/main/data/UC21_R1.fq.gz,https://raw.githubusercontent.com/rujinlong/test/main/data/UC21_R2.fq.gz
-UC24,https://raw.githubusercontent.com/rujinlong/test/main/data/UC24_R1.fq.gz,https://raw.githubusercontent.com/rujinlong/test/main/data/UC24_R2.fq.gz
-UC26,https://raw.githubusercontent.com/rujinlong/test/main/data/UC26_R1.fq.gz,https://raw.githubusercontent.com/rujinlong/test/main/data/UC26_R2.fq.gz
-UC28,https://raw.githubusercontent.com/rujinlong/test/main/data/UC28_R1.fq.gz,https://raw.githubusercontent.com/rujinlong/test/main/data/UC28_R2.fq.gz
-UC29,https://raw.githubusercontent.com/rujinlong/test/main/data/UC29_R1.fq.gz,https://raw.githubusercontent.com/rujinlong/test/main/data/UC29_R2.fq.gz
-UC30,https://raw.githubusercontent.com/rujinlong/test/main/data/UC30_R1.fq.gz,https://raw.githubusercontent.com/rujinlong/test/main/data/UC30_R2.fq.gz
-UC31,https://raw.githubusercontent.com/rujinlong/test/main/data/UC31_R1.fq.gz,https://raw.githubusercontent.com/rujinlong/test/main/data/UC31_R2.fq.gz
-UC32,https://raw.githubusercontent.com/rujinlong/test/main/data/UC32_R1.fq.gz,https://raw.githubusercontent.com/rujinlong/test/main/data/UC32_R2.fq.gz
+UC24,https://raw.githubusercontent.com/rujinlong/test/main/data/UC24_R1.fq.gz,https://raw.githubusercontent.com/rujinlong/test/main/data/UC24_R2.fq.gz

assets/samplesheet_testfull.csv

@@ -14,4 +14,4 @@ UC28,https://raw.githubusercontent.com/rujinlong/test/main/data/UC28_R1.fq.gz,ht
 UC29,https://raw.githubusercontent.com/rujinlong/test/main/data/UC29_R1.fq.gz,https://raw.githubusercontent.com/rujinlong/test/main/data/UC29_R2.fq.gz
 UC30,https://raw.githubusercontent.com/rujinlong/test/main/data/UC30_R1.fq.gz,https://raw.githubusercontent.com/rujinlong/test/main/data/UC30_R2.fq.gz
 UC31,https://raw.githubusercontent.com/rujinlong/test/main/data/UC31_R1.fq.gz,https://raw.githubusercontent.com/rujinlong/test/main/data/UC31_R2.fq.gz
-UC32,https://raw.githubusercontent.com/rujinlong/test/main/data/UC32_R1.fq.gz,https://raw.githubusercontent.com/rujinlong/test/main/data/UC32_R2.fq.gz
+UC32,https://raw.githubusercontent.com/rujinlong/test/main/data/UC32_R1.fq.gz,https://raw.githubusercontent.com/rujinlong/test/main/data/UC32_R2.fq.gz

conf/test.config

@@ -21,48 +21,4 @@ params {
 
     // Input data for minimal test
     input = "https://raw.githubusercontent.com/deng-lab/viroprofiler/main/assets/samplesheet.csv"
-    outdir = "output"
-    mode = "all"
-
-    // =============================  Database  ====================================
-    db = "${HOME}/viroprofiler"
-
-    // =============================  Decontamination  =============================
-    decontam = null
-    decontam_min_similarity = 0.95
-    contamref_idx = "${HOME}/viroprofiler/contamination_refs/hg19/ref"
-
-
-    // =============================  Contig library  ==============================
-    assembler = "spades"
-    assemblies = "scaffolds"  // [contigs, scaffolds]
-    contig_minlen = 3000
-    contig_cluster_min_similarity = 95
-    contig_cluster_min_coverage = 85
-
-    // =============================   Gene library   ==============================
-    prot_cluster_min_similarity = 0.7    // Minimum similarity of protein AA seqs in the same cluster
-    prot_cluster_min_coverage = 0.9    // Minimum similarity of protein AA seqs in the same cluster
-    gene_cluster_min_similarity = 0.9    // Minimum similarity of gene DNA seqs in the same cluster
-    gene_cluster_min_coverage = 0.9   // Minimum similarity of gene DNA seqs in the same cluster
-
-    // =============================  Binning  =====================================
-    binning = null   // "phamb", "vrhyme" or null
-    binning_minlen_contig = 3000
-    binning_minlen_bin = 3000
-    dvf_qvalue = 0.1
-
-
-    // =============================  Viral detection  =============================
-    // virsorter2_groups = "dsDNAphage,NCLDV,RNA,ssDNA,lavidaviridae"
-    virsorter2_groups = "dsDNAphage"
-
-    // =============================  Taxonomy  ====================================
-    contig_minlen_vcontact2 = 10000
-    pc_inflation = 1.5
-    vc_inflation = 1.5
-    taxa_db_source = "NCBI"
-
-    // =============================  Replication cycle  ===========================
-    replicyc = "bacphlip"    // "replidec" or "bacphlip"
 }