Merging template updates

`nf-core lint` overall result: Failed :x:

Updated for pipeline commit c41df66

+| ✅ 119 tests passed       |+
!| ❗ 26 tests had warnings |!
-| ❌ 42 tests failed       |-

### :x: Test failures: * [Test #15](https://nf-co.re/errors#15) - Param `read_pairs` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `read_singles` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `csv_pairs` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `csv_singles` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `fastas` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `protein_fastas` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `sra` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `tenx_tgz` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `tenx_tags` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `tenx_cell_barcode_pattern` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `tenx_molecular_barcode_pattern` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `tenx_min_umi_per_cell` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `molecules` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `ksizes` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `track_abundance` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `sketch_num_hashes` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `sketch_num_hashes_log2` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `sketch_scaled` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `sketch_scaled_log2` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `skip_compare` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `skip_compute` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `skip_trimming` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `translate_peptide_ksize` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `translate_peptide_molecule` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `translate_jaccard_threshold` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `reference_proteome_fasta` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `bloomfilter_tablesize` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `remove_ribo_rna` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `save_non_rrna_reads` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `rrna_database_manifest` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `split_kmer` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `subsample` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `save_fastas` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `write_barcode_meta_csv` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `bam` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `barcodes_file` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `rename_10x_barcodes` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `shard_size` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `input_paths` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `fasta_paths` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `protein_fasta_paths` from `nextflow config` not found in nextflow_schema.json * [Test #15](https://nf-co.re/errors#15) - Param `skip_multiqc` from `nextflow config` not found in nextflow_schema.json ### :heavy_exclamation_mark: Test warnings: * [Test #5](https://nf-co.re/errors#5) - GitHub Actions AWS full test should test full datasets: `/home/runner/work/kmermaid/kmermaid/.github/workflows/awsfulltest.yml` * [Test #6](https://nf-co.re/errors#6) - README did not have a Nextflow minimum version badge. * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `conda-forge::python=3.7.3`, `3.9.0` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `conda-forge::markdown=3.1.1`, `3.3.3` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `conda-forge::pymdown-extensions=6.0`, `8.0.1` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `conda-forge::pygments=2.5.2`, `2.7.2` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `conda-forge::tqdm=4.43.0`, `4.51.0` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `conda-forge::gxx_linux-64=7.3.0`, `9.3.0` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `conda-forge::s3fs=0.4.2`, `0.5.1` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `bioconda::samtools=1.10`, `1.11` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `bioconda::pysam=0.16.0`, `0.16.0.1` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `fastp=0.20.0`, `0.20.1` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `matplotlib=3.1.1`, `3.3.2` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `multiqc=1.8`, `1.9` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `numpy=1.17.5`, `1.19.2` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `pathos=0.2.5`, `0.2.6` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `pip=20.0.2`, `20.2.4` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `pytest=5.3.4`, `6.1.2` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `sphinx=2.3.1`, `3.2.1` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `sortmerna=2.1b`, `4.2.0` available * [Test #10](https://nf-co.re/errors#10) - TODO string found in `main.nf`: _If not using MultiQC, strip out this code (including params.max_multiqc_email_size)_ * [Test #15](https://nf-co.re/errors#15) - Schema param `single_end` not found from nextflow config * [Test #15](https://nf-co.re/errors#15) - Schema param `genome` not found from nextflow config * [Test #15](https://nf-co.re/errors#15) - Schema param `fasta` not found from nextflow config * [Test #15](https://nf-co.re/errors#15) - Schema param `igenomes_base` not found from nextflow config * [Test #15](https://nf-co.re/errors#15) - Schema param `igenomes_ignore` not found from nextflow config ### :white_check_mark: Tests passed: * [Test #1](https://nf-co.re/errors#1) - File found: `nextflow.config` * [Test #1](https://nf-co.re/errors#1) - File found: `nextflow_schema.json` * [Test #1](https://nf-co.re/errors#1) - File found: `LICENSE` or `LICENSE.md` or `LICENCE` or `LICENCE.md` * [Test #1](https://nf-co.re/errors#1) - File found: `README.md` * [Test #1](https://nf-co.re/errors#1) - File found: `CHANGELOG.md` * [Test #1](https://nf-co.re/errors#1) - File found: `docs/README.md` * [Test #1](https://nf-co.re/errors#1) - File found: `docs/output.md` * [Test #1](https://nf-co.re/errors#1) - File found: `docs/usage.md` * [Test #1](https://nf-co.re/errors#1) - File found: `.github/workflows/branch.yml` * [Test #1](https://nf-co.re/errors#1) - File found: `.github/workflows/ci.yml` * [Test #1](https://nf-co.re/errors#1) - File found: `.github/workflows/linting.yml` * [Test #1](https://nf-co.re/errors#1) - File found: `main.nf` * [Test #1](https://nf-co.re/errors#1) - File found: `environment.yml` * [Test #1](https://nf-co.re/errors#1) - File found: `Dockerfile` * [Test #1](https://nf-co.re/errors#1) - File found: `conf/base.config` * [Test #1](https://nf-co.re/errors#1) - File found: `.github/workflows/awstest.yml` * [Test #1](https://nf-co.re/errors#1) - File found: `.github/workflows/awsfulltest.yml` * [Test #1](https://nf-co.re/errors#1) - File not found check: `Singularity` * [Test #1](https://nf-co.re/errors#1) - File not found check: `parameters.settings.json` * [Test #1](https://nf-co.re/errors#1) - File not found check: `bin/markdown_to_html.r` * [Test #1](https://nf-co.re/errors#1) - File not found check: `.travis.yml` * [Test #3](https://nf-co.re/errors#3) - Licence check passed * [Test #2](https://nf-co.re/errors#2) - Dockerfile check passed * [Test #4](https://nf-co.re/errors#4) - Config variable found: `manifest.name` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `manifest.nextflowVersion` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `manifest.description` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `manifest.version` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `manifest.homePage` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `timeline.enabled` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `trace.enabled` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `report.enabled` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `dag.enabled` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `process.cpus` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `process.memory` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `process.time` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `params.outdir` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `params.input` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `manifest.mainScript` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `timeline.file` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `trace.file` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `report.file` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `dag.file` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `process.container` * [Test #4](https://nf-co.re/errors#4) - Config variable (correctly) not found: `params.version` * [Test #4](https://nf-co.re/errors#4) - Config variable (correctly) not found: `params.nf_required_version` * [Test #4](https://nf-co.re/errors#4) - Config variable (correctly) not found: `params.container` * [Test #4](https://nf-co.re/errors#4) - Config variable (correctly) not found: `params.singleEnd` * [Test #4](https://nf-co.re/errors#4) - Config variable (correctly) not found: `params.igenomesIgnore` * [Test #4](https://nf-co.re/errors#4) - Config `timeline.enabled` had correct value: `true` * [Test #4](https://nf-co.re/errors#4) - Config `report.enabled` had correct value: `true` * [Test #4](https://nf-co.re/errors#4) - Config `trace.enabled` had correct value: `true` * [Test #4](https://nf-co.re/errors#4) - Config `dag.enabled` had correct value: `true` * [Test #4](https://nf-co.re/errors#4) - Config `manifest.name` began with `nf-core/` * [Test #4](https://nf-co.re/errors#4) - Config variable `manifest.homePage` began with https://github.com/nf-core/ * [Test #4](https://nf-co.re/errors#4) - Config `dag.file` ended with `.svg` * [Test #4](https://nf-co.re/errors#4) - Config variable `manifest.nextflowVersion` started with >= or !>= * [Test #4](https://nf-co.re/errors#4) - Config `process.container` looks correct: `nfcore/kmermaid:dev` * [Test #4](https://nf-co.re/errors#4) - Config `manifest.version` ends in `dev`: `'0.1.0dev'` * [Test #5](https://nf-co.re/errors#5) - GitHub Actions 'branch' workflow is triggered for PRs to master: `/home/runner/work/kmermaid/kmermaid/.github/workflows/branch.yml` * [Test #5](https://nf-co.re/errors#5) - GitHub Actions 'branch' workflow looks good: `/home/runner/work/kmermaid/kmermaid/.github/workflows/branch.yml` * [Test #5](https://nf-co.re/errors#5) - GitHub Actions CI is triggered on expected events: `/home/runner/work/kmermaid/kmermaid/.github/workflows/ci.yml` * [Test #5](https://nf-co.re/errors#5) - CI is building the correct docker image: `docker build --no-cache . -t nfcore/kmermaid:dev` * [Test #5](https://nf-co.re/errors#5) - CI is pulling the correct docker image: docker pull nfcore/kmermaid:dev * [Test #5](https://nf-co.re/errors#5) - CI is tagging docker image correctly: docker tag nfcore/kmermaid:dev nfcore/kmermaid:dev * [Test #5](https://nf-co.re/errors#5) - Continuous integration checks minimum NF version: `/home/runner/work/kmermaid/kmermaid/.github/workflows/ci.yml` * [Test #5](https://nf-co.re/errors#5) - GitHub Actions linting workflow is triggered on PR and push: `/home/runner/work/kmermaid/kmermaid/.github/workflows/linting.yml` * [Test #5](https://nf-co.re/errors#5) - Continuous integration runs Markdown lint Tests: `/home/runner/work/kmermaid/kmermaid/.github/workflows/linting.yml` * [Test #5](https://nf-co.re/errors#5) - Continuous integration runs nf-core lint Tests: `/home/runner/work/kmermaid/kmermaid/.github/workflows/linting.yml` * [Test #5](https://nf-co.re/errors#5) - GitHub Actions AWS test is triggered on workflow_dispatch: `/home/runner/work/kmermaid/kmermaid/.github/workflows/awstest.yml` * [Test #5](https://nf-co.re/errors#5) - GitHub Actions AWS full test is triggered only on published release and workflow_dispatch: `/home/runner/work/kmermaid/kmermaid/.github/workflows/awsfulltest.yml` * [Test #6](https://nf-co.re/errors#6) - README had a bioconda badge * [Test #8](https://nf-co.re/errors#8) - Conda environment name was correct (nf-core-kmermaid-0.1.0dev) * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `conda-forge::python=3.7.3` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `conda-forge::markdown=3.1.1` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `conda-forge::pymdown-extensions=6.0` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `conda-forge::pygments=2.5.2` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `conda-forge::tqdm=4.43.0` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `conda-forge::gxx_linux-64=7.3.0` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `conda-forge::s3fs=0.4.2` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `bioconda::sourmash=3.5.0` * [Test #8](https://nf-co.re/errors#8) - Conda package is latest available: `bioconda::sourmash=3.5.0` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `bioconda::samtools=1.10` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `bioconda::screed=1.0.4` * [Test #8](https://nf-co.re/errors#8) - Conda package is latest available: `bioconda::screed=1.0.4` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `bioconda::khmer=3.0.0a3` * [Test #8](https://nf-co.re/errors#8) - Conda package is latest available: `bioconda::khmer=3.0.0a3` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `bioconda::pysam=0.16.0` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `anaconda::make=4.2.1` * [Test #8](https://nf-co.re/errors#8) - Conda package is latest available: `anaconda::make=4.2.1` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `alabaster=0.7.12` * [Test #8](https://nf-co.re/errors#8) - Conda package is latest available: `alabaster=0.7.12` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `fastp=0.20.0` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `fastqc=0.11.9` * [Test #8](https://nf-co.re/errors#8) - Conda package is latest available: `fastqc=0.11.9` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `matplotlib=3.1.1` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `multiqc=1.8` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `numpy=1.17.5` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `pathos=0.2.5` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `pip=20.0.2` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `pytest=5.3.4` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `seqtk=1.3` * [Test #8](https://nf-co.re/errors#8) - Conda package is latest available: `seqtk=1.3` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `ska=1.0` * [Test #8](https://nf-co.re/errors#8) - Conda package is latest available: `ska=1.0` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `sphinx=2.3.1` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `jupyter=1.0.0` * [Test #8](https://nf-co.re/errors#8) - Conda package is latest available: `jupyter=1.0.0` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `sortmerna=2.1b` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `ripgrep=12.1.1` * [Test #8](https://nf-co.re/errors#8) - Conda package is latest available: `ripgrep=12.1.1` * [Test #8](https://nf-co.re/errors#8) - Pip dependency had pinned version number: bam2fasta==1.0.8 * [Test #8](https://nf-co.re/errors#8) - PyPi package is latest available: 1.0.8 * [Test #8](https://nf-co.re/errors#8) - Pip dependency had pinned version number: sencha==1.0.3 * [Test #8](https://nf-co.re/errors#8) - PyPi package is latest available: 1.0.3 * [Test #9](https://nf-co.re/errors#9) - Found all expected strings in Dockerfile file * [Test #12](https://nf-co.re/errors#12) - Name adheres to nf-core convention * [Test #13](https://nf-co.re/errors#13) - Did not find any cookiecutter template strings (57 files) * [Test #14](https://nf-co.re/errors#14) - Schema lint passed * [Test #14](https://nf-co.re/errors#14) - Schema title + description lint passed ### Run details: * nf-core/tools version 1.11 * Run at `2020-10-29 22:33:21`

nf-core / kmermaid