diff --git a/episodes/12-nfcore.md b/episodes/12-nfcore.md index 1adc8248..f93cf9a2 100644 --- a/episodes/12-nfcore.md +++ b/episodes/12-nfcore.md @@ -9,7 +9,7 @@ exercises: 10 - Understand what nf-core is and how it relates to Nextflow. - Use the nf-core helper tool to find nf-core pipelines. - Understand how to configuration nf-core pipelines. -- Run a small nf-core pipeline using a test dataset. +- Run a small demo nf-core pipeline using a test dataset. :::::::::::::::::::::::::::::::::::::::::::::::::: @@ -40,19 +40,6 @@ nf-core pipelines are an organised collection of Nextflow scripts, other non-ne nf-core provides a suite of helper tools aim to help people run and develop pipelines. The [nf-core tools](https://nf-co.re/tools) package is written in Python and can run from the command line or imported and used within other packages. -::::::::::::::::::::::::::::::::::::::::: callout - -### Automatic version check - -nf-core/tools automatically checks the web to see if there is a new version of nf-core/tools available. If you would -prefer to skip this check, set the environment variable NFCORE\_NO\_VERSION\_CHECK. For example: - -```bash -export NFCORE_NO_VERSION_CHECK=1 -``` - -:::::::::::::::::::::::::::::::::::::::::::::::::: - #### nf-core tools sub-commands You can use the `--help` option to see the range of nf-core tools sub-commands. @@ -60,7 +47,7 @@ In this episode we will be covering the `list`, `launch` and `download` sub-comm aid in the finding and deployment of the nf-core pipelines. ```bash -$ nf-core --help +nf-core --help ``` ```output @@ -70,29 +57,40 @@ $ nf-core --help | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' - nf-core/tools version 2.1 - - - -Usage: nf-core [OPTIONS] COMMAND [ARGS]... - -Options: - --version Show the version and exit. - -v, --verbose Print verbose output to the console. - -l, --log-file Save a verbose log to a file. - --help Show this message and exit. - -Commands: - list List available nf-core pipelines with local info. - launch Launch a pipeline using a web GUI or command line prompts. - download Download a pipeline, nf-core/configs and pipeline... - licences List software licences for a given workflow. - create Create a new pipeline using the nf-core template. - lint Check pipeline code against nf-core guidelines. - modules Tools to manage Nextflow DSL2 modules as hosted on... - schema Suite of tools for developers to manage pipeline schema. - bump-version Update nf-core pipeline version number. - sync Sync a pipeline TEMPLATE branch with the nf-core template. + nf-core/tools version 2.14.1 - https://nf-co.re + + + + Usage: nf-core [OPTIONS] COMMAND [ARGS]... + + nf-core/tools provides a set of helper tools for use with nf-core Nextflow pipelines. + It is designed for both end-users running pipelines and also developers creating new pipelines. + +╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮ +│ --version Show the version and exit. │ +│ --verbose -v Print verbose output to the console. │ +│ --hide-progress Don't show progress bars. │ +│ --log-file -l Save a verbose log to a file. │ +│ --help -h Show this message and exit. │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭─ Commands for users ─────────────────────────────────────────────────────────────────────────────╮ +│ list List available nf-core pipelines with local info. │ +│ launch Launch a pipeline using a web GUI or command line prompts. │ +│ create-params-file Build a parameter file for a pipeline. │ +│ download Download a pipeline, nf-core/configs and pipeline singularity images. │ +│ licences List software licences for a given workflow (DSL1 only). │ +│ tui Open Textual TUI. │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭─ Commands for developers ────────────────────────────────────────────────────────────────────────╮ +│ create Create a new pipeline using the nf-core template. │ +│ lint Check pipeline code against nf-core guidelines. │ +│ modules Commands to manage Nextflow DSL2 modules (tool wrappers). │ +│ subworkflows Commands to manage Nextflow DSL2 subworkflows (tool wrappers). │ +│ schema Suite of tools for developers to manage pipeline schema. │ +│ create-logo Generate a logo with the nf-core logo template. │ +│ bump-version Update nf-core pipeline version number. │ +│ sync Sync a pipeline TEMPLATE branch with the nf-core template. │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ ``` ### Listing available nf-core pipelines @@ -105,7 +103,7 @@ If the pipeline has been pulled locally using Nextflow, it tells you when that w Run the command below. ```bash -$ nf-core list +nf-core list ``` An example of the output from the command is as follows: @@ -119,21 +117,22 @@ An example of the output from the command is as follows: | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' - nf-core/tools version 2.1 - - - - ┏━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━┓ - ┃ Pipeline Name ┃ Stars ┃ Latest Release ┃ Released ┃ Last Pulled ┃ Have latest release? ┃ - ┡━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━┩ - │ mhcquant │ 14 │ 2.0.0 │ 4 days ago │ - │ - │ - │ bacass │ 28 │ 2.0.0 │ 2 weeks ago │ - │ - │ - │ viralrecon │ 48 │ 2.2 │ 1 months ago │ - │ - │ - │ rnaseq │ 364 │ 3.3 │ 1 months ago │ - │ - │ - │ mag │ 63 │ 2.1.0 │ 1 months ago │ - │ - │ - │ fetchngs │ 25 │ 1.2 │ 1 months ago │ - │ - │ - │ bcellmagic │ 14 │ 2.0.0 │ 2 months ago │ - │ - │ - │ ampliseq │ 67 │ 2.0.0 │ 2 months ago │ - │ - │ + nf-core/tools version 2.14.1 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━┓ +┃ Pipeline Name ┃ Stars ┃ Latest Release ┃ Released ┃ Last Pulled ┃ Have latest release? ┃ +┡━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━┩ +│ mcmicro │ 4 │ dev │ 2 days ago │ - │ - │ +│ fastquorum │ 13 │ 1.0.0 │ 2 months ago │ - │ - │ +│ rnaseq │ 821 │ 3.14.0 │ 6 months ago │ - │ - │ +│ crisprseq │ 22 │ 2.2.0 │ 1 months ago │ - │ - │ +│ funcscan │ 62 │ 1.1.6 │ 2 weeks ago │ - │ - │ +│ pairgenomealign │ 0 │ dev │ 3 days ago │ - │ - │ +│ multiplesequencealign │ 11 │ dev │ 3 days ago │ - │ - │ +│ denovotranscript │ 0 │ dev │ 3 days ago │ - │ - │ +│ demo │ 1 │ 1.0.0 │ 1 months ago │ - │ - │ +│ demultiplex │ 37 │ 1.4.1 │ 5 months ago │ - │ - │ [..truncated..] ``` @@ -145,7 +144,7 @@ If you supply additional keywords after the `list` sub-command, the listed pipel Here we filter on the keywords **rna** and **rna-seq** . ```bash -$ nf-core list rna rna-seq +nf-core list rna rna-seq ``` ```output @@ -156,21 +155,26 @@ $ nf-core list rna rna-seq | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' - nf-core/tools version 2.1 + nf-core/tools version 2.14.1 - https://nf-co.re - -┏━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━┓ -┃ Pipeline Name ┃ Stars ┃ Latest Release ┃ Released ┃ Last Pulled ┃ Have latest release? ┃ -┡━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━┩ -│ rnaseq │ 364 │ 3.3 │ 1 months ago │ - │ - │ -│ smrnaseq │ 26 │ 1.1.0 │ 3 months ago │ - │ - │ -│ dualrnaseq │ 4 │ 1.0.0 │ 7 months ago │ - │ - │ -│ rnafusion │ 60 │ 1.2.0 │ 1 years ago │ - │ - │ -│ circrna │ 8 │ dev │ - │ - │ - │ -│ lncpipe │ 22 │ dev │ - │ - │ - │ -│ scflow │ 6 │ dev │ - │ - │ - │ -└───────────────┴───────┴────────────────┴──────────────┴─────────────┴──────────────────────┘ +┏━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━┓ +┃ Pipeline Name ┃ Stars ┃ Latest Release ┃ Released ┃ Last Pulled ┃ Have latest release? ┃ +┡━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━┩ +│ rnaseq │ 821 │ 3.14.0 │ 6 months ago │ - │ - │ +│ denovotranscript │ 0 │ dev │ 3 days ago │ - │ - │ +│ scnanoseq │ 5 │ dev │ 4 days ago │ - │ - │ +│ circrna │ 43 │ dev │ 6 days ago │ - │ - │ +│ smrnaseq │ 70 │ 2.3.1 │ 3 months ago │ - │ - │ +│ scrnaseq │ 185 │ 2.7.0 │ 4 weeks ago │ - │ - │ +│ differentialabundance │ 47 │ 1.5.0 │ 2 months ago │ - │ - │ +│ rnafusion │ 132 │ 3.0.2 │ 3 months ago │ - │ - │ +│ spatialvi │ 45 │ dev │ 2 months ago │ - │ - │ +│ rnasplice │ 35 │ 1.0.4 │ 2 months ago │ - │ - │ +│ dualrnaseq │ 16 │ 1.0.0 │ 3 years ago │ - │ - │ +│ marsseq │ 4 │ 1.0.3 │ 1 years ago │ - │ - │ +│ lncpipe │ 30 │ dev │ 2 years ago │ - │ - │ +└───────────────────────┴───────┴────────────────┴──────────────┴─────────────┴──────────────────────┘ ``` #### Sorting available nf-core pipelines @@ -189,21 +193,26 @@ nf-core list rna rna-seq --sort stars | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' -nf-core/tools version 2.1 - + nf-core/tools version 2.14.1 - https://nf-co.re -┏━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━┓ -┃ Pipeline Name ┃ Stars ┃ Latest Release ┃ Released ┃ Last Pulled ┃ Have latest release? ┃ -┡━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━┩ -│ rnaseq │ 364 │ 3.3 │ 1 months ago │ - │ - │ -│ rnafusion │ 60 │ 1.2.0 │ 1 years ago │ - │ - │ -│ smrnaseq │ 26 │ 1.1.0 │ 3 months ago │ - │ - │ -│ lncpipe │ 22 │ dev │ - │ - │ - │ -│ circrna │ 8 │ dev │ - │ - │ - │ -│ scflow │ 6 │ dev │ - │ - │ - │ -│ dualrnaseq │ 4 │ 1.0.0 │ 7 months ago │ - │ - │ -└───────────────┴───────┴────────────────┴──────────────┴─────────────┴──────────────────────┘ +┏━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━┓ +┃ Pipeline Name ┃ Stars ┃ Latest Release ┃ Released ┃ Last Pulled ┃ Have latest release? ┃ +┡━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━┩ +│ rnaseq │ 821 │ 3.14.0 │ 6 months ago │ - │ - │ +│ scrnaseq │ 185 │ 2.7.0 │ 4 weeks ago │ - │ - │ +│ rnafusion │ 132 │ 3.0.2 │ 3 months ago │ - │ - │ +│ smrnaseq │ 70 │ 2.3.1 │ 3 months ago │ - │ - │ +│ differentialabundance │ 47 │ 1.5.0 │ 2 months ago │ - │ - │ +│ spatialvi │ 45 │ dev │ 2 months ago │ - │ - │ +│ circrna │ 43 │ dev │ 6 days ago │ - │ - │ +│ rnasplice │ 35 │ 1.0.4 │ 2 months ago │ - │ - │ +│ lncpipe │ 30 │ dev │ 2 years ago │ - │ - │ +│ dualrnaseq │ 16 │ 1.0.0 │ 3 years ago │ - │ - │ +│ scnanoseq │ 5 │ dev │ 4 days ago │ - │ - │ +│ marsseq │ 4 │ 1.0.3 │ 1 years ago │ - │ - │ +│ denovotranscript │ 0 │ dev │ 3 days ago │ - │ - │ +└───────────────────────┴───────┴────────────────┴──────────────┴─────────────┴──────────────────────┘ ``` ::::::::::::::::::::::::::::::::::::::::: callout @@ -263,18 +272,15 @@ Unless you are actively developing pipeline code, you should use Nextflow's [bui $ nextflow pull nf-core/ ``` -Nextflow will also automatically fetch the pipeline code when you run +**Note** Nextflow will also automatically fetch the pipeline code when use `nextflow run nf-core/` command. -```bash -$ nextflow run nf-core/`. -``` For the best reproducibility, it is good to explicitly reference the pipeline version number that you wish to use with the `-revision`/`-r` flag. In the example below we are pulling the rnaseq pipeline version 3.0 ```bash -$ nextflow pull nf-core/rnaseq -revision 3.0 +nextflow pull nf-core/rnaseq -revision 3.14.0 ``` We can check the pipeline has been pulled using the `nf-core list` command. @@ -292,14 +298,13 @@ We can see from the output we have the latest release. | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' -nf-core/tools version 2.1 - + nf-core/tools version 2.14.1 - https://nf-co.re -┏━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━┓ -┃ Pipeline Name ┃ Stars ┃ Latest Release ┃ Released ┃ Last Pulled ┃ Have latest release? ┃ -┡━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━┩ -│ rnaseq │ 394 │ 3.4 │ 4 weeks ago │ 1 minutes ago │ Yes (v3.4) │ +┏━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━┓ +┃ Pipeline Name ┃ Stars ┃ Latest Release ┃ Released ┃ Last Pulled ┃ Have latest release? ┃ +┡━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━┩ +│ rnaseq │ 821 │ 3.14.0 │ 6 months ago │ 59 seconds ago │ Yes (v3.14.0) │ [..truncated..] ``` @@ -350,7 +355,7 @@ Each pipeline has its own webpage at [https://nf-co.re/](https://nf-co.re/)\` syntax. ```bash -$ nextflow run nf-core/rnaseq -r 3.0 --email "my@email.com"` +nextflow run nf-core/rnaseq -r 3.14.0 --email "my@email.com"` ``` #### Config Profiles @@ -472,8 +474,8 @@ Configuration files can contain the definition of one or more profiles. A profil Multiple profiles are comma-separated. When there are differing configuration settings provided by different profiles, the right-most profile takes priority. ```bash -$ nextflow run nf-core/rnaseq -r 3.0 -profile test,conda -$ nextflow run nf-core/rnaseq -r 3.0 -profile , test, conda +nextflow run nf-core/rnaseq -r 3.14.0 -profile test,conda +nextflow run nf-core/rnaseq -r 3.14.0 -profile , test, conda ``` **Note** The order in which config profiles are specified matters. Their priority increases from left to right. @@ -491,7 +493,7 @@ Be clever with multiple Nextflow configuration locations. For example, use `-pro ### Exercise create a custom config -Add the `params.email` to a file called `nfcore-custom.config` +Add the `params.email` to a file called `nfcore-custom.config` ::::::::::::::: solution @@ -512,7 +514,7 @@ params.email = "myemail@address.com" The nf-core config profile `test` is special profile, which defines a minimal data set and configuration, that runs quickly and tests the workflow from beginning to end. Since the data is minimal, the output is often nonsense. Real world example output are instead linked on the nf-core pipeline web page, where the workflow has been run with a full size data set: ```bash -$ nextflow run nf-core/ -profile test +nextflow run nf-core/ -profile test ``` ::::::::::::::::::::::::::::::::::::::::: callout @@ -536,12 +538,11 @@ By default, the pipeline will download the pipeline code and the institutional n If you specify the flag `--singularity`, it will also download any singularity image files that are required (this needs Singularity to be installed). All files are saved to a single directory, ready to be transferred to the cluster where the pipeline will be executed. -``` -$ nf-core download nf-core/rnaseq -r 3.4 +```bash +nf-core download nf-core/rnaseq -r 3.14.0 ``` -> -```bash +```output ,--./,-. ___ __ __ __ ___ /,-._.--~\ @@ -549,90 +550,104 @@ $ nf-core download nf-core/rnaseq -r 3.4 | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' - nf-core/tools version 2.1 + nf-core/tools version 2.14.1 - https://nf-co.re + +WARNING Could not find GitHub authentication token. Some API requests may fail. +? Include the nf-core's default institutional configuration files into the download? No +In addition to the pipeline code, this tool can download software containers. +? Download software container images: none -INFO Saving nf-core/rnaseq download.py:148 - Pipeline release: '3.4' - Pull singularity containers: 'No' - Output file: 'nf-core-rnaseq-3.4.tar.gz' -INFO Downloading workflow files from GitHub download.py:151 -INFO Downloading centralised configs from GitHub download.py:155 -INFO Compressing download.. download.py:166 -INFO Command to extract files: tar -xzf nf-core-rnaseq-3.4.tar.gz download.py:653 -INFO MD5 checksum for nf-core-rnaseq-3.4.tar.gz: f0e0c239bdb39c613d6a080f1dee88e9 +If transferring the downloaded files to another system, it can be convenient to have everything compressed in a single file. +? Choose compression type: none +INFO Saving 'nf-core/rnaseq' + Pipeline revision: '3.14.0' + Use containers: 'none' + Container library: 'quay.io' + Output directory: 'nf-core-rnaseq_3.14.0' + Include default institutional configuration: 'False' +INFO Downloading workflow files from GitHub ``` ::::::::::::::::::::::::::::::::::::::: challenge -### Exercise Run a test nf-core pipeline +### Exercise Run a demo nf-core pipeline -Run the nf-core/hlatyping pipeline release 1.2.0 with the provided test data using the profile `test` and `conda`. -Add the parameter `--max_memory 3G` on the command line. +Run the `nf-core/demo` pipeline release 1.0.0 with the provided test data using the profile `test`. +Add the parameters `--max_memory 3G`, `--skip_trim`, and --outdir "nfcore-demo-out" on the command line. Include the config file, `nfcore-custom.config`, from the previous exercise using the option `-c`, to send an email when your pipeline finishes. -``` -$ nextflow run nf-core/hlatyping -r 1.2.0 -profile test,conda --max_memory 3G -c nfcore-custom.config +```bash +$ nextflow run nf-core/demo -r 1.0.0 -profile test --skip_trim --max_memory 3.GB -c nfcore-custom.config ``` -The pipeline does next-generation sequencing-based Human Leukozyte Antigen (HLA) typing and should run quickly. +The `nf-core/demo` pipleine is a simple nf-core style bioinformatics pipeline for workshops and demonstrations that runs FASTQC and multiqc. ::::::::::::::: solution ### Solution ```output - N E X T F L O W ~ version 21.04.0 -Launching `nf-core/hlatyping` [pedantic_engelbart] - revision: 6998794795 [1.2.0] -BAM file format detected. Initiate remapping to HLA alleles with yara mapper. ----------------------------------------------------- - ,--./,-. - ___ __ __ __ ___ /,-._.--~' - |\ | |__ __ / ` / \ |__) |__ } { - | \| | \__, \__/ | \ |___ \`-._,-`-, - `._,._,' -nf-core/hlatyping v1.2.0 ----------------------------------------------------- - -Pipeline Release : 1.2.0 -Run Name : pedantic_engelbart -File Type : BAM -Seq Type : dna -Index Location : /home/training/.nextflow/assets/nf-core/hlatyping/data/indices/yara/hla_reference_dna -IP Solver : glpk -Enumerations : 1 -Beta : 0.009 -Max Memory : 3G -Max CPUs : 2 -Max Time : 2d -Input : https://github.com/nf-core/test-datasets/raw/hlatyping/bam/example_pe.bam -Data Type : Paired-End -Output Dir : results -Launch Dir : /home/training -Working Dir : /home/training/work -Script Dir : /home/training/.nextflow/assets/nf-core/hlatyping -User : training -Max Resources : 3G memory, 2 cpus, 2d time per job -Config Profile : conda,test -Config Profile Description: Minimal test dataset to check pipeline function -Config Files : /home/training/.nextflow/assets/nf-core/hlatyping/nextflow.config, /home/training/nextflow.config, /home/training/.nextflow/assets/nf-> > > >core/hlatyping/nextflow.config ----------------------------------------------------- -BAM file format detected. Initiate remapping to HLA alleles with yara mapper. -[- ] process > remap_to_hla - -executor > local (6) -[05/084b41] process > remap_to_hla (1) [100%] 1 of 1 ✔ -[5a/9bec8b] process > make_ot_config [100%] 1 of 1 ✔ -[54/8bc5d7] process > run_optitype (1) [100%] 1 of 1 ✔ -[a9/2cbea8] process > output_documentation [100%] 1 of 1 ✔ -[df/d3dac5] process > get_software_versions [100%] 1 of 1 ✔ -[e1/903ed9] process > multiqc (1) [100%] 1 of 1 ✔ --[nf-core/hlatyping] Pipeline completed successfully- -WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info. -Completed at: 26-Oct-2021 10:07:27 -Duration : 4m 14s -CPU hours : (a few seconds) -Succeeded : 6 + N E X T F L O W ~ version 24.04.3 + +Launching `https://github.com/nf-core/demo` [silly_bohr] DSL2 - revision: 705f18e4b1 [master] + +WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value` + + +------------------------------------------------------ + ,--./,-. + ___ __ __ __ ___ /,-._.--~' + |\ | |__ __ / ` / \ |__) |__ } { + | \| | \__, \__/ | \ |___ \`-._,-`-, + `._,._,' + nf-core/demo v1.0.0-g705f18e +------------------------------------------------------ +Core Nextflow options + revision : master + runName : silly_bohr + launchDir : /home/nf-training + workDir : /home/nf-training/work + projectDir : /home/nf-training/.nextflow/assets/nf-core/demo + userName : nf-training + profile : test + configFiles : + +Input/output options + input : https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv + outdir : out + email : myemail@address.com + +Process skipping options + skip_trim : true + +Institutional config options + config_profile_name : Test profile + config_profile_description: Minimal test dataset to check pipeline function + +Max job request options + max_cpus : 2 + max_memory : 3.GB + max_time : 6.h + +!! Only displaying parameters that differ from the pipeline defaults !! +------------------------------------------------------ +If you use nf-core/demo for your analysis please cite: + +* The pipeline + +* The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x + +* Software dependencies + https://github.com/nf-core/demo/blob/master/CITATIONS.md +------------------------------------------------------ +executor > local (4) +[08/94286a] process > NFCORE_DEMO:DEMO:FASTQC (SAMPLE2_PE) [100%] 3 of 3 ✔ +[df/45c5c7] process > NFCORE_DEMO:DEMO:MULTIQC [100%] 1 of 1 ✔ +-[nf-core/demo] Sent summary e-mail to graeme.grimes@ed.ac.uk (sendmail)- +-[nf-core/demo] Pipeline completed successfully- ``` :::::::::::::::::::::::::