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Lint warnings #220

Closed
ewels opened this issue Feb 4, 2021 · 2 comments
Closed

Lint warnings #220

ewels opened this issue Feb 4, 2021 · 2 comments
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bug Something isn't working

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@ewels
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ewels commented Feb 4, 2021

Hi all,

Just a heads up that your nf-core lint tests are throwing quite a lot of warnings (although getting a little ✅ still).

The vast majority are for outdated conda packages which may or may not be possible to resolve, but there are a few that look like they could do with some attention:

  • Test #5 - GitHub Actions AWS full test should test full datasets: /home/runner/work/ampliseq/ampliseq/.github/workflows/awsfulltest.yml
  • Test #10 - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • Test #10 - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • Test #10 - TODO string in awstest.yml: You can customise CI pipeline run tests as required
  • Test #10 - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • Test #10 - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed

I'd hoped that these results would show up as comments on PRs automatically after nf-core/tools release v1.12 (nf-core/tools#765) but I guess they're not 😞

Anyway, full lint output from #219 below:

nf-core lint overall result: Passed ✅

Posted for pipeline commit 5152da0

+| ✅ 521 tests passed       |+
!| ❗ 251 tests had warnings |!

❗ Test warnings:

  • Test #5 - GitHub Actions AWS full test should test full datasets: /home/runner/work/ampliseq/ampliseq/.github/workflows/awsfulltest.yml
  • Test #8 - Conda dep outdated: conda-forge::markdown=3.1.1, 3.3.3 available
  • Test #8 - Conda dep outdated: conda-forge::pymdown-extensions=6.0, 8.1.1 available
  • Test #8 - Conda dep outdated: fastqc=0.11.8, 0.11.9 available
  • Test #8 - Conda dep outdated: r-rmarkdown=1.18, 2.6 available
  • Test #8 - Conda dep outdated: r-optparse=1.6.4, 1.6.6 available
  • Test #8 - Conda dep outdated: ncurses=6.1, 6.2 available
  • Test #8 - Conda dep outdated: biopython=1.77, 1.78 available
  • Test #8 - Conda dep outdated: alsa-lib=1.1.5, 1.2.3 available
  • Test #8 - Conda dep outdated: asn1crypto=1.2.0, 1.4.0 available
  • Test #8 - Conda dep outdated: atomicwrites=1.3.0, 1.4.0 available
  • Test #8 - Conda dep outdated: attrs=19.3.0, 20.3.0 available
  • Test #8 - Conda dep outdated: backcall=0.1.0, 0.2.0 available
  • Test #8 - Conda dep outdated: binutils_impl_linux-64=2.31.1, 2.35.1 available
  • Test #8 - Conda dep outdated: binutils_linux-64=2.31.1, 2.35 available
  • Test #8 - Conda dep outdated: bioconductor-biobase=2.42.0, 2.50.0 available
  • Test #8 - Conda dep outdated: bioconductor-biocgenerics=0.28.0, 0.36.0 available
  • Test #8 - Conda dep outdated: bioconductor-biocparallel=1.16.6, 1.24.0 available
  • Test #8 - Conda dep outdated: bioconductor-biostrings=2.50.2, 2.58.0 available
  • Test #8 - Conda dep outdated: bioconductor-dada2=1.10.0, 1.18.0 available
  • Test #8 - Conda dep outdated: bioconductor-delayedarray=0.8.0, 0.16.0 available
  • Test #8 - Conda dep outdated: bioconductor-genomeinfodb=1.18.1, 1.26.0 available
  • Test #8 - Conda dep outdated: bioconductor-genomeinfodbdata=1.2.1, 1.2.4 available
  • Test #8 - Conda dep outdated: bioconductor-genomicalignments=1.18.1, 1.26.0 available
  • Test #8 - Conda dep outdated: bioconductor-genomicranges=1.34.0, 1.42.0 available
  • Test #8 - Conda dep outdated: bioconductor-iranges=2.16.0, 2.24.0 available
  • Test #8 - Conda dep outdated: bioconductor-rsamtools=1.34.0, 2.6.0 available
  • Test #8 - Conda dep outdated: bioconductor-s4vectors=0.20.1, 0.28.0 available
  • Test #8 - Conda dep outdated: bioconductor-shortread=1.40.0, 1.48.0 available
  • Test #8 - Conda dep outdated: bioconductor-summarizedexperiment=1.12.0, 1.20.0 available
  • Test #8 - Conda dep outdated: bioconductor-xvector=0.22.0, 0.30.0 available
  • Test #8 - Conda dep outdated: bioconductor-zlibbioc=1.28.0, 1.36.0 available
  • Test #8 - Conda dep outdated: conda-forge::biom-format=2.1.7, 2.1.10 available
  • Test #8 - Conda dep outdated: blas=2.14, 2.108 available
  • Test #8 - Conda dep outdated: blast=2.9.0, 2.10.1 available
  • Test #8 - Conda dep outdated: bleach=3.1.0, 3.3.0 available
  • Test #8 - Conda dep outdated: bokeh=1.3.4, 2.2.3 available
  • Test #8 - Conda dep outdated: boost=1.68.0, 1.74.0 available
  • Test #8 - Conda dep outdated: boost-cpp=1.68.0, 1.74.0 available
  • Test #8 - Conda dep outdated: bwidget=1.9.13, 1.9.14 available
  • Test #8 - Conda dep outdated: ca-certificates=2019.9.11, 2020.12.5 available
  • Test #8 - Conda dep outdated: cachecontrol=0.12.5, 0.12.6 available
  • Test #8 - Conda dep outdated: certifi=2019.9.11, 2020.12.5 available
  • Test #8 - Conda dep outdated: cffi=1.13.1, 1.14.4 available
  • Test #8 - Conda dep outdated: chardet=3.0.4, 4.0.0 available
  • Test #8 - Conda dep outdated: click=7.0, 7.1.2 available
  • Test #8 - Conda dep outdated: cryptography=2.7, 3.3.1 available
  • Test #8 - Conda dep outdated: curl=7.65.3, 7.71.1 available
  • Test #8 - Conda dep outdated: cutadapt=2.8, 3.2 available
  • Test #8 - Conda dep outdated: cython=0.29.13, 0.29.21 available
  • Test #8 - Conda dep outdated: decorator=4.4.1, 4.4.2 available
  • Test #8 - Conda dep outdated: dendropy=4.4.0, 4.5.1 available
  • Test #8 - Conda dep outdated: dnaio=0.4, 0.5.0 available
  • Test #8 - Conda dep outdated: emperor=1.0.0b20, 1.0.2 available
  • Test #8 - Conda dep outdated: expat=2.2.5, 2.2.10 available
  • Test #8 - Conda dep outdated: fastcluster=1.1.25, 1.1.26 available
  • Test #8 - Conda dep outdated: freetype=2.10.0, 2.10.4 available
  • Test #8 - Conda dep outdated: gcc_impl_linux-64=7.3.0, 9.3.0 available
  • Test #8 - Conda dep outdated: gcc_linux-64=7.3.0, 9.3.0 available
  • Test #8 - Conda dep outdated: gfortran_impl_linux-64=7.3.0, 9.3.0 available
  • Test #8 - Conda dep outdated: gfortran_linux-64=7.3.0, 9.3.0 available
  • Test #8 - Conda dep outdated: giflib=5.1.7, 5.2.1 available
  • Test #8 - Conda dep outdated: glib=2.58.3, 2.66.5 available
  • Test #8 - Conda dep outdated: gmp=6.1.2, 6.2.1 available
  • Test #8 - Conda dep outdated: gnutls=3.6.5, 3.6.13 available
  • Test #8 - Conda dep outdated: gsl=2.5, 2.6 available
  • Test #8 - Conda dep outdated: gst-plugins-base=1.14.5, 1.18.3 available
  • Test #8 - Conda dep outdated: gstreamer=1.14.5, 1.18.3 available
  • Test #8 - Conda dep outdated: gxx_impl_linux-64=7.3.0, 9.3.0 available
  • Test #8 - Conda dep outdated: gxx_linux-64=7.3.0, 9.3.0 available
  • Test #8 - Conda dep outdated: h5py=2.10.0, 3.1.0 available
  • Test #8 - Conda dep outdated: harfbuzz=2.4.0, 2.7.4 available
  • Test #8 - Conda dep outdated: hdf5=1.10.5, 1.12.0 available
  • Test #8 - Conda dep outdated: hdmedians=0.13, 0.14.1 available
  • Test #8 - Conda dep outdated: hmmer=3.1b2, 3.3.2 available
  • Test #8 - Conda dep outdated: icu=58.2, 68.1 available
  • Test #8 - Conda dep outdated: idna=2.8, 3.1 available
  • Test #8 - Conda dep outdated: conda-forge::ijson=2.5, 3.1.3 available
  • Test #8 - Conda dep outdated: importlib_metadata=0.23, 3.4.0 available
  • Test #8 - Conda dep outdated: ipykernel=5.1.3, 5.4.3 available
  • Test #8 - Conda dep outdated: ipython=7.9.0, 7.20.0 available
  • Test #8 - Conda dep outdated: ipywidgets=7.5.1, 7.6.3 available
  • Test #8 - Conda dep outdated: iqtree=1.6.12, 2.0.3 available
  • Test #8 - Conda dep outdated: jedi=0.15.1, 0.18.0 available
  • Test #8 - Conda dep outdated: jinja2=2.10.3, 2.11.3 available
  • Test #8 - Conda dep outdated: joblib=0.14.0, 1.0.0 available
  • Test #8 - Conda dep outdated: jpeg=9c, 9d available
  • Test #8 - Conda dep outdated: jsonschema=3.1.1, 3.2.0 available
  • Test #8 - Conda dep outdated: jupyter_client=5.3.3, 6.1.11 available
  • Test #8 - Conda dep outdated: jupyter_core=4.5.0, 4.7.1 available
  • Test #8 - Conda dep outdated: kiwisolver=1.1.0, 1.3.1 available
  • Test #8 - Conda dep outdated: krb5=1.16.3, 1.17.2 available
  • Test #8 - Conda dep outdated: lcms2=2.9, 2.11 available
  • Test #8 - Conda dep outdated: libblas=3.8.0, 3.9.0 available
  • Test #8 - Conda dep outdated: libcblas=3.8.0, 3.9.0 available
  • Test #8 - Conda dep outdated: libcurl=7.65.3, 7.71.1 available
  • Test #8 - Conda dep outdated: libedit=3.1.20170329, 3.1.20191231 available
  • Test #8 - Conda dep outdated: libffi=3.2.1, 3.3 available
  • Test #8 - Conda dep outdated: libgfortran-ng=7.3.0, 9.3.0 available
  • Test #8 - Conda dep outdated: libiconv=1.15, 1.16 available
  • Test #8 - Conda dep outdated: liblapack=3.8.0, 3.9.0 available
  • Test #8 - Conda dep outdated: liblapacke=3.8.0, 3.9.0 available
  • Test #8 - Conda dep outdated: libopenblas=0.3.7, 0.3.13 available
  • Test #8 - Conda dep outdated: libsodium=1.0.17, 1.0.18 available
  • Test #8 - Conda dep outdated: libssh2=1.8.2, 1.9.0 available
  • Test #8 - Conda dep outdated: libtiff=4.0.10, 4.2.0 available
  • Test #8 - Conda dep outdated: libxml2=2.9.9, 2.9.10 available
  • Test #8 - Conda dep outdated: lz4-c=1.8.3, 1.9.3 available
  • Test #8 - Conda dep outdated: mafft=7.310, 7.475 available
  • Test #8 - Conda dep outdated: make=4.2.1, 4.3 available
  • Test #8 - Conda dep outdated: matplotlib=3.1.0, 3.3.4 available
  • Test #8 - Conda dep outdated: matplotlib-base=3.1.0, 3.3.4 available
  • Test #8 - Conda dep outdated: more-itertools=7.2.0, 8.6.0 available
  • Test #8 - Conda dep outdated: msgpack-python=0.6.2, 1.0.2 available
  • Test #8 - Conda dep outdated: natsort=6.0.0, 7.1.1 available
  • Test #8 - Conda dep outdated: nbconvert=5.6.1, 6.0.7 available
  • Test #8 - Conda dep outdated: nbformat=4.4.0, 5.1.2 available
  • Test #8 - Conda dep outdated: ncurses=6.1, 6.2 available
  • Test #8 - Conda dep outdated: nettle=3.4.1, 3.7 available
  • Test #8 - Conda dep outdated: networkx=2.4, 2.5 available
  • Test #8 - Conda dep outdated: notebook=6.0.1, 6.2.0 available
  • Test #8 - Conda dep outdated: numpy=1.17.3, 1.20.0 available
  • Test #8 - Conda dep outdated: openjdk=11.0.1, 11.0.8 available
  • Test #8 - Conda dep outdated: openssl=1.1.1c, 1.1.1i available
  • Test #8 - Conda dep outdated: packaging=19.2, 20.8 available
  • Test #8 - Conda dep outdated: pandas=0.25.2, 1.2.1 available
  • Test #8 - Conda dep outdated: pandoc=2.7.3, 2.11.4 available
  • Test #8 - Conda dep outdated: pango=1.40.14, 1.42.4 available
  • Test #8 - Conda dep outdated: parso=0.5.1, 0.8.1 available
  • Test #8 - Conda dep outdated: pcre=8.43, 8.44 available
  • Test #8 - Conda dep outdated: perl=5.26.2, 5.32.0.1 available
  • Test #8 - Conda dep outdated: perl-json-xs=2.34, 4.02 available
  • Test #8 - Conda dep outdated: pexpect=4.7.0, 4.8.0 available
  • Test #8 - Conda dep outdated: pigz=2.3.4, 2.5 available
  • Test #8 - Conda dep outdated: pillow=6.2.1, 8.1.0 available
  • Test #8 - Conda dep outdated: pip=19.3.1, 21.0.1 available
  • Test #8 - Conda dep outdated: pixman=0.38.0, 0.40.0 available
  • Test #8 - Conda dep outdated: pluggy=0.12.0, 0.13.1 available
  • Test #8 - Conda dep outdated: prometheus_client=0.7.1, 0.9.0 available
  • Test #8 - Conda dep outdated: prompt_toolkit=2.0.10, 3.0.14 available
  • Test #8 - Conda dep outdated: psutil=5.6.3, 5.8.0 available
  • Test #8 - Conda dep outdated: ptyprocess=0.6.0, 0.7.0 available
  • Test #8 - Conda dep outdated: py=1.8.0, 1.10.0 available
  • Test #8 - Conda dep outdated: pycparser=2.19, 2.20 available
  • Test #8 - Conda dep outdated: pygments=2.4.2, 2.7.4 available
  • Test #8 - Conda dep outdated: pyopenssl=19.0.0, 20.0.1 available
  • Test #8 - Conda dep outdated: pyparsing=2.4.2, 2.4.7 available
  • Test #8 - Conda dep outdated: pyqt=5.9.2, 5.12.3 available
  • Test #8 - Conda dep outdated: pyrsistent=0.15.5, 0.17.3 available
  • Test #8 - Conda dep outdated: pytest=5.2.2, 6.2.2 available
  • Test #8 - Conda dep outdated: python=3.6.7, 3.9.1 available
  • Test #8 - Conda dep outdated: python-dateutil=2.8.0, 2.8.1 available
  • Test #8 - Conda dep outdated: pytz=2019.3, 2021.1 available
  • Test #8 - Conda dep outdated: pyyaml=5.1.2, 5.4.1 available
  • Test #8 - Conda dep outdated: pyzmq=18.1.0, 22.0.1 available
  • Test #8 - Conda dep outdated: q2-alignment=2019.10.0, 2020.11.1 available
  • Test #8 - Conda dep outdated: q2-composition=2019.10.0, 2020.11.1 available
  • Test #8 - Conda dep outdated: q2-cutadapt=2019.10.0, 2020.11.1 available
  • Test #8 - Conda dep outdated: q2-dada2=2019.10.0, 2020.11.1 available
  • Test #8 - Conda dep outdated: q2-deblur=2019.10.0, 2020.11.1 available
  • Test #8 - Conda dep outdated: q2-demux=2019.10.0, 2020.11.1 available
  • Test #8 - Conda dep outdated: q2-diversity=2019.10.0, 2020.11.1 available
  • Test #8 - Conda dep outdated: q2-emperor=2019.10.0, 2020.11.1 available
  • Test #8 - Conda dep outdated: q2-feature-classifier=2019.10.0, 2020.11.1 available
  • Test #8 - Conda dep outdated: q2-feature-table=2019.10.0, 2020.11.1 available
  • Test #8 - Conda dep outdated: q2-fragment-insertion=2019.10.0, 2020.11.1 available
  • Test #8 - Conda dep outdated: q2-gneiss=2019.10.0, 2020.11.1 available
  • Test #8 - Conda dep outdated: q2-longitudinal=2019.10.0, 2020.11.1 available
  • Test #8 - Conda dep outdated: q2-metadata=2019.10.0, 2020.11.1 available
  • Test #8 - Conda dep outdated: q2-phylogeny=2019.10.0, 2020.11.1 available
  • Test #8 - Conda dep outdated: q2-quality-control=2019.10.0, 2020.11.1 available
  • Test #8 - Conda dep outdated: q2-quality-filter=2019.10.0, 2020.11.1 available
  • Test #8 - Conda dep outdated: q2-sample-classifier=2019.10.0, 2020.11.1 available
  • Test #8 - Conda dep outdated: q2-taxa=2019.10.0, 2020.11.1 available
  • Test #8 - Conda dep outdated: q2-types=2019.10.0, 2020.11.1 available
  • Test #8 - Conda dep outdated: q2-vsearch=2019.10.0, 2020.11.1 available
  • Test #8 - Conda dep outdated: q2cli=2019.10.0, 2020.11.1 available
  • Test #8 - Conda dep outdated: q2templates=2019.10.0, 2020.11.1 available
  • Test #8 - Conda dep outdated: qiime2=2019.10.0, 2020.11.1 available
  • Test #8 - Conda dep outdated: qt=5.9.7, 5.12.9 available
  • Test #8 - Conda dep outdated: r-backports=1.1.5, 1.2.1 available
  • Test #8 - Conda dep outdated: r-base=3.5.1, 4.0.3 available
  • Test #8 - Conda dep outdated: r-bh=1.69.0_1, 1.75.0_0 available
  • Test #8 - Conda dep outdated: r-cli=1.1.0, 2.3.0 available
  • Test #8 - Conda dep outdated: r-colorspace=1.4_1, 2.0_0 available
  • Test #8 - Conda dep outdated: r-crayon=1.3.4, 1.4.0 available
  • Test #8 - Conda dep outdated: r-data.table=1.12.6, 1.13.6 available
  • Test #8 - Conda dep outdated: r-digest=0.6.22, 0.6.27 available
  • Test #8 - Conda dep outdated: r-ellipsis=0.3.0, 0.3.1 available
  • Test #8 - Conda dep outdated: r-fansi=0.4.0, 0.4.2 available
  • Test #8 - Conda dep outdated: r-ggplot2=3.2.1, 3.3.3 available
  • Test #8 - Conda dep outdated: r-glue=1.3.1, 1.4.2 available
  • Test #8 - Conda dep outdated: r-labeling=0.3, 0.4.2 available
  • Test #8 - Conda dep outdated: r-lattice=0.20_38, 0.20_41 available
  • Test #8 - Conda dep outdated: r-latticeextra=0.6_28, 0.6_29 available
  • Test #8 - Conda dep outdated: r-magrittr=1.5, 2.0.1 available
  • Test #8 - Conda dep outdated: r-mass=7.3_51.4, 7.3_53 available
  • Test #8 - Conda dep outdated: r-matrix=1.2_17, 1.3_2 available
  • Test #8 - Conda dep outdated: r-matrixstats=0.55.0, 0.58.0 available
  • Test #8 - Conda dep outdated: r-mgcv=1.8_29, 1.8_33 available
  • Test #8 - Conda dep outdated: r-nlme=3.1_141, 3.1_152 available
  • Test #8 - Conda dep outdated: r-pillar=1.4.2, 1.4.7 available
  • Test #8 - Conda dep outdated: r-plyr=1.8.4, 1.8.6 available
  • Test #8 - Conda dep outdated: r-r6=2.4.0, 2.5.0 available
  • Test #8 - Conda dep outdated: r-rcpp=1.0.2, 1.0.6 available
  • Test #8 - Conda dep outdated: r-rcppparallel=4.4.4, 5.0.2 available
  • Test #8 - Conda dep outdated: r-rcurl=1.95_4.12, 1.98_1.2 available
  • Test #8 - Conda dep outdated: r-reshape2=1.4.3, 1.4.4 available
  • Test #8 - Conda dep outdated: r-rlang=0.4.1, 0.4.10 available
  • Test #8 - Conda dep outdated: r-scales=1.0.0, 1.1.1 available
  • Test #8 - Conda dep outdated: r-stringi=1.4.3, 1.5.3 available
  • Test #8 - Conda dep outdated: r-tibble=2.1.3, 3.0.6 available
  • Test #8 - Conda dep outdated: r-vctrs=0.2.0, 0.3.6 available
  • Test #8 - Conda dep outdated: r-vegan=2.5_6, 2.5_7 available
  • Test #8 - Conda dep outdated: r-withr=2.1.2, 2.4.1 available
  • Test #8 - Conda dep outdated: requests=2.22.0, 2.25.1 available
  • Test #8 - Conda dep outdated: conda-forge::scikit-bio=0.5.5, 0.5.6 available
  • Test #8 - Conda dep outdated: scikit-learn=0.21.2, 0.24.1 available
  • Test #8 - Conda dep outdated: scipy=1.3.1, 1.6.0 available
  • Test #8 - Conda dep outdated: seaborn=0.9.0, 0.11.1 available
  • Test #8 - Conda dep outdated: setuptools=41.6.0, 50.0.0 available
  • Test #8 - Conda dep outdated: sina=1.6.0, 1.7.2 available
  • Test #8 - Conda dep outdated: sip=4.19.8, 4.19.24 available
  • Test #8 - Conda dep outdated: six=1.12.0, 1.15.0 available
  • Test #8 - Conda dep outdated: sortmerna=2.0, 4.2.0 available
  • Test #8 - Conda dep outdated: sqlite=3.30.1, 3.34.0 available
  • Test #8 - Conda dep outdated: statsmodels=0.10.1, 0.12.2 available
  • Test #8 - Conda dep outdated: tbb=2019.9, 2020.2 available
  • Test #8 - Conda dep outdated: terminado=0.8.2, 0.9.2 available
  • Test #8 - Conda dep outdated: testpath=0.4.2, 0.4.4 available
  • Test #8 - Conda dep outdated: tk=8.6.9, 8.6.10 available
  • Test #8 - Conda dep outdated: tornado=6.0.3, 6.1 available
  • Test #8 - Conda dep outdated: traitlets=4.3.3, 5.0.5 available
  • Test #8 - Conda dep outdated: conda-forge::tzlocal=2.0.0, 2.1 available
  • Test #8 - Conda dep outdated: unifrac=0.10.0, 0.20.1 available
  • Test #8 - Conda dep outdated: urllib3=1.25.6, 1.26.3 available
  • Test #8 - Conda dep outdated: vsearch=2.7.0, 2.15.1 available
  • Test #8 - Conda dep outdated: wcwidth=0.1.7, 0.2.5 available
  • Test #8 - Conda dep outdated: wheel=0.33.6, 0.36.2 available
  • Test #8 - Conda dep outdated: xopen=0.8.4, 1.1.0 available
  • Test #8 - Conda dep outdated: xorg-libx11=1.6.9, 1.7.0 available
  • Test #8 - Conda dep outdated: xz=5.2.4, 5.2.5 available
  • Test #8 - Conda dep outdated: yaml=0.1.7, 0.2.5 available
  • Test #8 - Conda dep outdated: zeromq=4.3.2, 4.3.4 available
  • Test #8 - Conda dep outdated: zipp=0.6.0, 3.4.0 available
  • Test #8 - Conda dep outdated: zstd=1.4.3, 1.4.8 available
  • Test #10 - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • Test #10 - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • Test #10 - TODO string in awstest.yml: You can customise CI pipeline run tests as required
  • Test #10 - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • Test #10 - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed

✅ Tests passed:

  • Test #1 - File found: nextflow.config
  • Test #1 - File found: nextflow_schema.json
  • Test #1 - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • Test #1 - File found: README.md
  • Test #1 - File found: CHANGELOG.md
  • Test #1 - File found: docs/README.md
  • Test #1 - File found: docs/output.md
  • Test #1 - File found: docs/usage.md
  • Test #1 - File found: .github/workflows/branch.yml
  • Test #1 - File found: .github/workflows/ci.yml
  • Test #1 - File found: .github/workflows/linting.yml
  • Test #1 - File found: main.nf
  • Test #1 - File found: environment.yml
  • Test #1 - File found: Dockerfile
  • Test #1 - File found: conf/base.config
  • Test #1 - File found: .github/workflows/awstest.yml
  • Test #1 - File found: .github/workflows/awsfulltest.yml
  • Test #1 - File not found check: Singularity
  • Test #1 - File not found check: parameters.settings.json
  • Test #1 - File not found check: bin/markdown_to_html.r
  • Test #1 - File not found check: .github/workflows/push_dockerhub.yml
  • Test #1 - File not found check: .travis.yml
  • Test #3 - Licence check passed
  • Test #2 - Dockerfile check passed
  • Test #4 - Config variable found: manifest.name
  • Test #4 - Config variable found: manifest.nextflowVersion
  • Test #4 - Config variable found: manifest.description
  • Test #4 - Config variable found: manifest.version
  • Test #4 - Config variable found: manifest.homePage
  • Test #4 - Config variable found: timeline.enabled
  • Test #4 - Config variable found: trace.enabled
  • Test #4 - Config variable found: report.enabled
  • Test #4 - Config variable found: dag.enabled
  • Test #4 - Config variable found: process.cpus
  • Test #4 - Config variable found: process.memory
  • Test #4 - Config variable found: process.time
  • Test #4 - Config variable found: params.outdir
  • Test #4 - Config variable found: params.input
  • Test #4 - Config variable found: manifest.mainScript
  • Test #4 - Config variable found: timeline.file
  • Test #4 - Config variable found: trace.file
  • Test #4 - Config variable found: report.file
  • Test #4 - Config variable found: dag.file
  • Test #4 - Config variable found: process.container
  • Test #4 - Config variable (correctly) not found: params.version
  • Test #4 - Config variable (correctly) not found: params.nf_required_version
  • Test #4 - Config variable (correctly) not found: params.container
  • Test #4 - Config variable (correctly) not found: params.singleEnd
  • Test #4 - Config variable (correctly) not found: params.igenomesIgnore
  • Test #4 - Config timeline.enabled had correct value: true
  • Test #4 - Config report.enabled had correct value: true
  • Test #4 - Config trace.enabled had correct value: true
  • Test #4 - Config dag.enabled had correct value: true
  • Test #4 - Config manifest.name began with nf-core/
  • Test #4 - Config variable manifest.homePage began with https://github.com/nf-core/
  • Test #4 - Config dag.file ended with .svg
  • Test #4 - Config variable manifest.nextflowVersion started with >= or !>=
  • Test #4 - Config process.container looks correct: nfcore/ampliseq:dev
  • Test #4 - Config manifest.version ends in dev: '1.3.0dev'
  • Test #5 - GitHub Actions 'branch' workflow is triggered for PRs to master: /home/runner/work/ampliseq/ampliseq/.github/workflows/branch.yml
  • Test #5 - GitHub Actions 'branch' workflow looks good: /home/runner/work/ampliseq/ampliseq/.github/workflows/branch.yml
  • Test #5 - GitHub Actions CI is triggered on expected events: /home/runner/work/ampliseq/ampliseq/.github/workflows/ci.yml
  • Test #5 - CI is building the correct docker image: docker build --no-cache . -t nfcore/ampliseq:dev
  • Test #5 - CI is pulling the correct docker image: docker pull nfcore/ampliseq:dev
  • Test #5 - CI is tagging docker image correctly: docker tag nfcore/ampliseq:dev nfcore/ampliseq:dev
  • Test #5 - Continuous integration checks minimum NF version: /home/runner/work/ampliseq/ampliseq/.github/workflows/ci.yml
  • Test #5 - GitHub Actions linting workflow is triggered on PR and push: /home/runner/work/ampliseq/ampliseq/.github/workflows/linting.yml
  • Test #5 - Continuous integration runs Markdown lint Tests: /home/runner/work/ampliseq/ampliseq/.github/workflows/linting.yml
  • Test #5 - Continuous integration runs nf-core lint Tests: /home/runner/work/ampliseq/ampliseq/.github/workflows/linting.yml
  • Test #5 - GitHub Actions AWS test is triggered on workflow_dispatch: /home/runner/work/ampliseq/ampliseq/.github/workflows/awstest.yml
  • Test #5 - GitHub Actions AWS full test is triggered only on published release and workflow_dispatch: /home/runner/work/ampliseq/ampliseq/.github/workflows/awsfulltest.yml
  • Test #6 - README Nextflow minimum version badge matched config. Badge: 20.04.0, Config: 20.04.0
  • Test #6 - README had a bioconda badge
  • Test #8 - Conda environment name was correct (nf-core-ampliseq-1.3.0dev)
  • Test #8 - Conda dep had pinned version number: conda-forge::markdown=3.1.1
  • Test #8 - Conda dep had pinned version number: conda-forge::pymdown-extensions=6.0
  • Test #8 - Conda dep had pinned version number: fastqc=0.11.8
  • Test #8 - Conda dep had pinned version number: font-ttf-dejavu-sans-mono=2.37
  • Test #8 - Conda package is the latest available: font-ttf-dejavu-sans-mono=2.37
  • Test #8 - Conda dep had pinned version number: multiqc=1.9
  • Test #8 - Conda package is the latest available: multiqc=1.9
  • Test #8 - Conda dep had pinned version number: unzip=6.0
  • Test #8 - Conda package is the latest available: unzip=6.0
  • Test #8 - Conda dep had pinned version number: r-rmarkdown=1.18
  • Test #8 - Conda dep had pinned version number: r-optparse=1.6.4
  • Test #8 - Conda dep had pinned version number: ncurses=6.1
  • Test #8 - Conda dep had pinned version number: biopython=1.77
  • Test #8 - Conda dep had pinned version number: _libgcc_mutex=0.1
  • Test #8 - Conda package is the latest available: _libgcc_mutex=0.1
  • Test #8 - Conda dep had pinned version number: _r-mutex=1.0.1
  • Test #8 - Conda package is the latest available: _r-mutex=1.0.1
  • Test #8 - Conda dep had pinned version number: alsa-lib=1.1.5
  • Test #8 - Conda dep had pinned version number: arb-bio-tools=6.0.6
  • Test #8 - Conda package is the latest available: arb-bio-tools=6.0.6
  • Test #8 - Conda dep had pinned version number: asn1crypto=1.2.0
  • Test #8 - Conda dep had pinned version number: atomicwrites=1.3.0
  • Test #8 - Conda dep had pinned version number: attrs=19.3.0
  • Test #8 - Conda dep had pinned version number: backcall=0.1.0
  • Test #8 - Conda dep had pinned version number: bibtexparser=1.1.0
  • Test #8 - Conda package is the latest available: bibtexparser=1.1.0
  • Test #8 - Conda dep had pinned version number: binutils_impl_linux-64=2.31.1
  • Test #8 - Conda dep had pinned version number: binutils_linux-64=2.31.1
  • Test #8 - Conda dep had pinned version number: bioconductor-biobase=2.42.0
  • Test #8 - Conda dep had pinned version number: bioconductor-biocgenerics=0.28.0
  • Test #8 - Conda dep had pinned version number: bioconductor-biocparallel=1.16.6
  • Test #8 - Conda dep had pinned version number: bioconductor-biostrings=2.50.2
  • Test #8 - Conda dep had pinned version number: bioconductor-dada2=1.10.0
  • Test #8 - Conda dep had pinned version number: bioconductor-delayedarray=0.8.0
  • Test #8 - Conda dep had pinned version number: bioconductor-genomeinfodb=1.18.1
  • Test #8 - Conda dep had pinned version number: bioconductor-genomeinfodbdata=1.2.1
  • Test #8 - Conda dep had pinned version number: bioconductor-genomicalignments=1.18.1
  • Test #8 - Conda dep had pinned version number: bioconductor-genomicranges=1.34.0
  • Test #8 - Conda dep had pinned version number: bioconductor-iranges=2.16.0
  • Test #8 - Conda dep had pinned version number: bioconductor-rsamtools=1.34.0
  • Test #8 - Conda dep had pinned version number: bioconductor-s4vectors=0.20.1
  • Test #8 - Conda dep had pinned version number: bioconductor-shortread=1.40.0
  • Test #8 - Conda dep had pinned version number: bioconductor-summarizedexperiment=1.12.0
  • Test #8 - Conda dep had pinned version number: bioconductor-xvector=0.22.0
  • Test #8 - Conda dep had pinned version number: bioconductor-zlibbioc=1.28.0
  • Test #8 - Conda dep had pinned version number: conda-forge::biom-format=2.1.7
  • Test #8 - Conda dep had pinned version number: blas=2.14
  • Test #8 - Conda dep had pinned version number: blast=2.9.0
  • Test #8 - Conda dep had pinned version number: bleach=3.1.0
  • Test #8 - Conda dep had pinned version number: bokeh=1.3.4
  • Test #8 - Conda dep had pinned version number: boost=1.68.0
  • Test #8 - Conda dep had pinned version number: boost-cpp=1.68.0
  • Test #8 - Conda dep had pinned version number: bwidget=1.9.13
  • Test #8 - Conda dep had pinned version number: bzip2=1.0.8
  • Test #8 - Conda package is the latest available: bzip2=1.0.8
  • Test #8 - Conda dep had pinned version number: ca-certificates=2019.9.11
  • Test #8 - Conda dep had pinned version number: cachecontrol=0.12.5
  • Test #8 - Conda dep had pinned version number: cairo=1.16.0
  • Test #8 - Conda package is the latest available: cairo=1.16.0
  • Test #8 - Conda dep had pinned version number: certifi=2019.9.11
  • Test #8 - Conda dep had pinned version number: cffi=1.13.1
  • Test #8 - Conda dep had pinned version number: chardet=3.0.4
  • Test #8 - Conda dep had pinned version number: click=7.0
  • Test #8 - Conda dep had pinned version number: cryptography=2.7
  • Test #8 - Conda dep had pinned version number: curl=7.65.3
  • Test #8 - Conda dep had pinned version number: cutadapt=2.8
  • Test #8 - Conda dep had pinned version number: cycler=0.10.0
  • Test #8 - Conda package is the latest available: cycler=0.10.0
  • Test #8 - Conda dep had pinned version number: cython=0.29.13
  • Test #8 - Conda dep had pinned version number: dbus=1.13.6
  • Test #8 - Conda package is the latest available: dbus=1.13.6
  • Test #8 - Conda dep had pinned version number: bioconda::deblur=1.1.0
  • Test #8 - Conda package is the latest available: bioconda::deblur=1.1.0
  • Test #8 - Conda dep had pinned version number: decorator=4.4.1
  • Test #8 - Conda dep had pinned version number: defusedxml=0.6.0
  • Test #8 - Conda package is the latest available: defusedxml=0.6.0
  • Test #8 - Conda dep had pinned version number: dendropy=4.4.0
  • Test #8 - Conda dep had pinned version number: dnaio=0.4
  • Test #8 - Conda dep had pinned version number: emperor=1.0.0b20
  • Test #8 - Conda dep had pinned version number: entrypoints=0.3
  • Test #8 - Conda package is the latest available: entrypoints=0.3
  • Test #8 - Conda dep had pinned version number: expat=2.2.5
  • Test #8 - Conda dep had pinned version number: fastcluster=1.1.25
  • Test #8 - Conda dep had pinned version number: fasttree=2.1.10
  • Test #8 - Conda package is the latest available: fasttree=2.1.10
  • Test #8 - Conda dep had pinned version number: fontconfig=2.13.1
  • Test #8 - Conda package is the latest available: fontconfig=2.13.1
  • Test #8 - Conda dep had pinned version number: freetype=2.10.0
  • Test #8 - Conda dep had pinned version number: future=0.18.2
  • Test #8 - Conda package is the latest available: future=0.18.2
  • Test #8 - Conda dep had pinned version number: gcc_impl_linux-64=7.3.0
  • Test #8 - Conda dep had pinned version number: gcc_linux-64=7.3.0
  • Test #8 - Conda dep had pinned version number: gettext=0.19.8.1
  • Test #8 - Conda package is the latest available: gettext=0.19.8.1
  • Test #8 - Conda dep had pinned version number: gfortran_impl_linux-64=7.3.0
  • Test #8 - Conda dep had pinned version number: gfortran_linux-64=7.3.0
  • Test #8 - Conda dep had pinned version number: giflib=5.1.7
  • Test #8 - Conda dep had pinned version number: glib=2.58.3
  • Test #8 - Conda dep had pinned version number: gmp=6.1.2
  • Test #8 - Conda dep had pinned version number: gneiss=0.4.6
  • Test #8 - Conda package is the latest available: gneiss=0.4.6
  • Test #8 - Conda dep had pinned version number: gnutls=3.6.5
  • Test #8 - Conda dep had pinned version number: graphite2=1.3.13
  • Test #8 - Conda package is the latest available: graphite2=1.3.13
  • Test #8 - Conda dep had pinned version number: gsl=2.5
  • Test #8 - Conda dep had pinned version number: gst-plugins-base=1.14.5
  • Test #8 - Conda dep had pinned version number: gstreamer=1.14.5
  • Test #8 - Conda dep had pinned version number: gxx_impl_linux-64=7.3.0
  • Test #8 - Conda dep had pinned version number: gxx_linux-64=7.3.0
  • Test #8 - Conda dep had pinned version number: h5py=2.10.0
  • Test #8 - Conda dep had pinned version number: harfbuzz=2.4.0
  • Test #8 - Conda dep had pinned version number: hdf5=1.10.5
  • Test #8 - Conda dep had pinned version number: hdmedians=0.13
  • Test #8 - Conda dep had pinned version number: hmmer=3.1b2
  • Test #8 - Conda dep had pinned version number: icu=58.2
  • Test #8 - Conda dep had pinned version number: idna=2.8
  • Test #8 - Conda dep had pinned version number: conda-forge::ijson=2.5
  • Test #8 - Conda dep had pinned version number: importlib_metadata=0.23
  • Test #8 - Conda dep had pinned version number: ipykernel=5.1.3
  • Test #8 - Conda dep had pinned version number: ipython=7.9.0
  • Test #8 - Conda dep had pinned version number: ipython_genutils=0.2.0
  • Test #8 - Conda package is the latest available: ipython_genutils=0.2.0
  • Test #8 - Conda dep had pinned version number: ipywidgets=7.5.1
  • Test #8 - Conda dep had pinned version number: iqtree=1.6.12
  • Test #8 - Conda dep had pinned version number: jedi=0.15.1
  • Test #8 - Conda dep had pinned version number: jinja2=2.10.3
  • Test #8 - Conda dep had pinned version number: joblib=0.14.0
  • Test #8 - Conda dep had pinned version number: jpeg=9c
  • Test #8 - Conda dep had pinned version number: jsonschema=3.1.1
  • Test #8 - Conda dep had pinned version number: jupyter_client=5.3.3
  • Test #8 - Conda dep had pinned version number: jupyter_core=4.5.0
  • Test #8 - Conda dep had pinned version number: kiwisolver=1.1.0
  • Test #8 - Conda dep had pinned version number: krb5=1.16.3
  • Test #8 - Conda dep had pinned version number: lcms2=2.9
  • Test #8 - Conda dep had pinned version number: libarbdb=6.0.6
  • Test #8 - Conda package is the latest available: libarbdb=6.0.6
  • Test #8 - Conda dep had pinned version number: libblas=3.8.0
  • Test #8 - Conda dep had pinned version number: libcblas=3.8.0
  • Test #8 - Conda dep had pinned version number: libcurl=7.65.3
  • Test #8 - Conda dep had pinned version number: libedit=3.1.20170329
  • Test #8 - Conda dep had pinned version number: libffi=3.2.1
  • Test #8 - Conda dep had pinned version number: libgcc=7.2.0
  • Test #8 - Conda package is the latest available: libgcc=7.2.0
  • Test #8 - Conda dep had pinned version number: anaconda::libgcc-ng=9.1.0
  • Test #8 - Conda package is the latest available: anaconda::libgcc-ng=9.1.0
  • Test #8 - Conda dep had pinned version number: libgfortran-ng=7.3.0
  • Test #8 - Conda dep had pinned version number: libiconv=1.15
  • Test #8 - Conda dep had pinned version number: liblapack=3.8.0
  • Test #8 - Conda dep had pinned version number: liblapacke=3.8.0
  • Test #8 - Conda dep had pinned version number: libopenblas=0.3.7
  • Test #8 - Conda dep had pinned version number: libpng=1.6.37
  • Test #8 - Conda package is the latest available: libpng=1.6.37
  • Test #8 - Conda dep had pinned version number: libsodium=1.0.17
  • Test #8 - Conda dep had pinned version number: libssh2=1.8.2
  • Test #8 - Conda dep had pinned version number: anaconda::libstdcxx-ng=9.1.0
  • Test #8 - Conda package is the latest available: anaconda::libstdcxx-ng=9.1.0
  • Test #8 - Conda dep had pinned version number: libtiff=4.0.10
  • Test #8 - Conda dep had pinned version number: libuuid=2.32.1
  • Test #8 - Conda package is the latest available: libuuid=2.32.1
  • Test #8 - Conda dep had pinned version number: libxcb=1.13
  • Test #8 - Conda package is the latest available: libxcb=1.13
  • Test #8 - Conda dep had pinned version number: libxml2=2.9.9
  • Test #8 - Conda dep had pinned version number: lockfile=0.12.2
  • Test #8 - Conda package is the latest available: lockfile=0.12.2
  • Test #8 - Conda dep had pinned version number: lz4-c=1.8.3
  • Test #8 - Conda dep had pinned version number: mafft=7.310
  • Test #8 - Conda dep had pinned version number: make=4.2.1
  • Test #8 - Conda dep had pinned version number: markupsafe=1.1.1
  • Test #8 - Conda package is the latest available: markupsafe=1.1.1
  • Test #8 - Conda dep had pinned version number: matplotlib=3.1.0
  • Test #8 - Conda dep had pinned version number: matplotlib-base=3.1.0
  • Test #8 - Conda dep had pinned version number: mistune=0.8.4
  • Test #8 - Conda package is the latest available: mistune=0.8.4
  • Test #8 - Conda dep had pinned version number: more-itertools=7.2.0
  • Test #8 - Conda dep had pinned version number: msgpack-python=0.6.2
  • Test #8 - Conda dep had pinned version number: natsort=6.0.0
  • Test #8 - Conda dep had pinned version number: nbconvert=5.6.1
  • Test #8 - Conda dep had pinned version number: nbformat=4.4.0
  • Test #8 - Conda dep had pinned version number: ncurses=6.1
  • Test #8 - Conda dep had pinned version number: nettle=3.4.1
  • Test #8 - Conda dep had pinned version number: networkx=2.4
  • Test #8 - Conda dep had pinned version number: nose=1.3.7
  • Test #8 - Conda package is the latest available: nose=1.3.7
  • Test #8 - Conda dep had pinned version number: notebook=6.0.1
  • Test #8 - Conda dep had pinned version number: numpy=1.17.3
  • Test #8 - Conda dep had pinned version number: olefile=0.46
  • Test #8 - Conda package is the latest available: olefile=0.46
  • Test #8 - Conda dep had pinned version number: openjdk=11.0.1
  • Test #8 - Conda dep had pinned version number: openssl=1.1.1c
  • Test #8 - Conda dep had pinned version number: packaging=19.2
  • Test #8 - Conda dep had pinned version number: pandas=0.25.2
  • Test #8 - Conda dep had pinned version number: pandoc=2.7.3
  • Test #8 - Conda dep had pinned version number: pandocfilters=1.4.2
  • Test #8 - Conda package is the latest available: pandocfilters=1.4.2
  • Test #8 - Conda dep had pinned version number: pango=1.40.14
  • Test #8 - Conda dep had pinned version number: parso=0.5.1
  • Test #8 - Conda dep had pinned version number: patsy=0.5.1
  • Test #8 - Conda package is the latest available: patsy=0.5.1
  • Test #8 - Conda dep had pinned version number: pcre=8.43
  • Test #8 - Conda dep had pinned version number: perl=5.26.2
  • Test #8 - Conda dep had pinned version number: perl-archive-tar=2.32
  • Test #8 - Conda package is the latest available: perl-archive-tar=2.32
  • Test #8 - Conda dep had pinned version number: perl-carp=1.38
  • Test #8 - Conda package is the latest available: perl-carp=1.38
  • Test #8 - Conda dep had pinned version number: perl-common-sense=3.74
  • Test #8 - Conda package is the latest available: perl-common-sense=3.74
  • Test #8 - Conda dep had pinned version number: perl-compress-raw-bzip2=2.087
  • Test #8 - Conda package is the latest available: perl-compress-raw-bzip2=2.087
  • Test #8 - Conda dep had pinned version number: perl-compress-raw-zlib=2.087
  • Test #8 - Conda package is the latest available: perl-compress-raw-zlib=2.087
  • Test #8 - Conda dep had pinned version number: perl-exporter=5.72
  • Test #8 - Conda package is the latest available: perl-exporter=5.72
  • Test #8 - Conda dep had pinned version number: perl-exporter-tiny=1.002001
  • Test #8 - Conda package is the latest available: perl-exporter-tiny=1.002001
  • Test #8 - Conda dep had pinned version number: perl-extutils-makemaker=7.36
  • Test #8 - Conda package is the latest available: perl-extutils-makemaker=7.36
  • Test #8 - Conda dep had pinned version number: perl-io-compress=2.087
  • Test #8 - Conda package is the latest available: perl-io-compress=2.087
  • Test #8 - Conda dep had pinned version number: perl-io-zlib=1.10
  • Test #8 - Conda package is the latest available: perl-io-zlib=1.10
  • Test #8 - Conda dep had pinned version number: perl-json=4.02
  • Test #8 - Conda package is the latest available: perl-json=4.02
  • Test #8 - Conda dep had pinned version number: perl-json-xs=2.34
  • Test #8 - Conda dep had pinned version number: perl-list-moreutils=0.428
  • Test #8 - Conda package is the latest available: perl-list-moreutils=0.428
  • Test #8 - Conda dep had pinned version number: perl-list-moreutils-xs=0.428
  • Test #8 - Conda package is the latest available: perl-list-moreutils-xs=0.428
  • Test #8 - Conda dep had pinned version number: perl-pathtools=3.75
  • Test #8 - Conda package is the latest available: perl-pathtools=3.75
  • Test #8 - Conda dep had pinned version number: perl-scalar-list-utils=1.52
  • Test #8 - Conda package is the latest available: perl-scalar-list-utils=1.52
  • Test #8 - Conda dep had pinned version number: perl-types-serialiser=1.0
  • Test #8 - Conda package is the latest available: perl-types-serialiser=1.0
  • Test #8 - Conda dep had pinned version number: perl-xsloader=0.24
  • Test #8 - Conda package is the latest available: perl-xsloader=0.24
  • Test #8 - Conda dep had pinned version number: pexpect=4.7.0
  • Test #8 - Conda dep had pinned version number: pickleshare=0.7.5
  • Test #8 - Conda package is the latest available: pickleshare=0.7.5
  • Test #8 - Conda dep had pinned version number: pigz=2.3.4
  • Test #8 - Conda dep had pinned version number: pillow=6.2.1
  • Test #8 - Conda dep had pinned version number: pip=19.3.1
  • Test #8 - Conda dep had pinned version number: pixman=0.38.0
  • Test #8 - Conda dep had pinned version number: pluggy=0.12.0
  • Test #8 - Conda dep had pinned version number: prometheus_client=0.7.1
  • Test #8 - Conda dep had pinned version number: prompt_toolkit=2.0.10
  • Test #8 - Conda dep had pinned version number: psutil=5.6.3
  • Test #8 - Conda dep had pinned version number: pthread-stubs=0.4
  • Test #8 - Conda package is the latest available: pthread-stubs=0.4
  • Test #8 - Conda dep had pinned version number: ptyprocess=0.6.0
  • Test #8 - Conda dep had pinned version number: py=1.8.0
  • Test #8 - Conda dep had pinned version number: pycparser=2.19
  • Test #8 - Conda dep had pinned version number: pygments=2.4.2
  • Test #8 - Conda dep had pinned version number: pyopenssl=19.0.0
  • Test #8 - Conda dep had pinned version number: pyparsing=2.4.2
  • Test #8 - Conda dep had pinned version number: pyqt=5.9.2
  • Test #8 - Conda dep had pinned version number: pyrsistent=0.15.5
  • Test #8 - Conda dep had pinned version number: pysocks=1.7.1
  • Test #8 - Conda package is the latest available: pysocks=1.7.1
  • Test #8 - Conda dep had pinned version number: pytest=5.2.2
  • Test #8 - Conda dep had pinned version number: python=3.6.7
  • Test #8 - Conda dep had pinned version number: python-dateutil=2.8.0
  • Test #8 - Conda dep had pinned version number: pytz=2019.3
  • Test #8 - Conda dep had pinned version number: pyyaml=5.1.2
  • Test #8 - Conda dep had pinned version number: pyzmq=18.1.0
  • Test #8 - Conda dep had pinned version number: q2-alignment=2019.10.0
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  • Test #8 - Conda dep had pinned version number: q2-cutadapt=2019.10.0
  • Test #8 - Conda dep had pinned version number: q2-dada2=2019.10.0
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  • Test #8 - Conda dep had pinned version number: q2-demux=2019.10.0
  • Test #8 - Conda dep had pinned version number: q2-diversity=2019.10.0
  • Test #8 - Conda dep had pinned version number: q2-emperor=2019.10.0
  • Test #8 - Conda dep had pinned version number: q2-feature-classifier=2019.10.0
  • Test #8 - Conda dep had pinned version number: q2-feature-table=2019.10.0
  • Test #8 - Conda dep had pinned version number: q2-fragment-insertion=2019.10.0
  • Test #8 - Conda dep had pinned version number: q2-gneiss=2019.10.0
  • Test #8 - Conda dep had pinned version number: q2-longitudinal=2019.10.0
  • Test #8 - Conda dep had pinned version number: q2-metadata=2019.10.0
  • Test #8 - Conda dep had pinned version number: q2-phylogeny=2019.10.0
  • Test #8 - Conda dep had pinned version number: q2-quality-control=2019.10.0
  • Test #8 - Conda dep had pinned version number: q2-quality-filter=2019.10.0
  • Test #8 - Conda dep had pinned version number: q2-sample-classifier=2019.10.0
  • Test #8 - Conda dep had pinned version number: q2-taxa=2019.10.0
  • Test #8 - Conda dep had pinned version number: q2-types=2019.10.0
  • Test #8 - Conda dep had pinned version number: q2-vsearch=2019.10.0
  • Test #8 - Conda dep had pinned version number: q2cli=2019.10.0
  • Test #8 - Conda dep had pinned version number: q2templates=2019.10.0
  • Test #8 - Conda dep had pinned version number: qiime2=2019.10.0
  • Test #8 - Conda dep had pinned version number: qt=5.9.7
  • Test #8 - Conda dep had pinned version number: r-assertthat=0.2.1
  • Test #8 - Conda package is the latest available: r-assertthat=0.2.1
  • Test #8 - Conda dep had pinned version number: r-backports=1.1.5
  • Test #8 - Conda dep had pinned version number: r-base=3.5.1
  • Test #8 - Conda dep had pinned version number: r-bh=1.69.0_1
  • Test #8 - Conda dep had pinned version number: r-bitops=1.0_6
  • Test #8 - Conda package is the latest available: r-bitops=1.0_6
  • Test #8 - Conda dep had pinned version number: r-cli=1.1.0
  • Test #8 - Conda dep had pinned version number: r-cluster=2.1.0
  • Test #8 - Conda package is the latest available: r-cluster=2.1.0
  • Test #8 - Conda dep had pinned version number: r-colorspace=1.4_1
  • Test #8 - Conda dep had pinned version number: r-crayon=1.3.4
  • Test #8 - Conda dep had pinned version number: r-data.table=1.12.6
  • Test #8 - Conda dep had pinned version number: r-digest=0.6.22
  • Test #8 - Conda dep had pinned version number: r-ellipsis=0.3.0
  • Test #8 - Conda dep had pinned version number: r-fansi=0.4.0
  • Test #8 - Conda dep had pinned version number: r-formatr=1.7
  • Test #8 - Conda package is the latest available: r-formatr=1.7
  • Test #8 - Conda dep had pinned version number: r-futile.logger=1.4.3
  • Test #8 - Conda package is the latest available: r-futile.logger=1.4.3
  • Test #8 - Conda dep had pinned version number: r-futile.options=1.0.1
  • Test #8 - Conda package is the latest available: r-futile.options=1.0.1
  • Test #8 - Conda dep had pinned version number: r-ggplot2=3.2.1
  • Test #8 - Conda dep had pinned version number: r-glue=1.3.1
  • Test #8 - Conda dep had pinned version number: r-gtable=0.3.0
  • Test #8 - Conda package is the latest available: r-gtable=0.3.0
  • Test #8 - Conda dep had pinned version number: r-hwriter=1.3.2
  • Test #8 - Conda package is the latest available: r-hwriter=1.3.2
  • Test #8 - Conda dep had pinned version number: r-labeling=0.3
  • Test #8 - Conda dep had pinned version number: r-lambda.r=1.2.4
  • Test #8 - Conda package is the latest available: r-lambda.r=1.2.4
  • Test #8 - Conda dep had pinned version number: r-lattice=0.20_38
  • Test #8 - Conda dep had pinned version number: r-latticeextra=0.6_28
  • Test #8 - Conda dep had pinned version number: r-lazyeval=0.2.2
  • Test #8 - Conda package is the latest available: r-lazyeval=0.2.2
  • Test #8 - Conda dep had pinned version number: r-magrittr=1.5
  • Test #8 - Conda dep had pinned version number: r-mass=7.3_51.4
  • Test #8 - Conda dep had pinned version number: r-matrix=1.2_17
  • Test #8 - Conda dep had pinned version number: r-matrixstats=0.55.0
  • Test #8 - Conda dep had pinned version number: r-mgcv=1.8_29
  • Test #8 - Conda dep had pinned version number: r-munsell=0.5.0
  • Test #8 - Conda package is the latest available: r-munsell=0.5.0
  • Test #8 - Conda dep had pinned version number: r-nlme=3.1_141
  • Test #8 - Conda dep had pinned version number: r-permute=0.9_5
  • Test #8 - Conda package is the latest available: r-permute=0.9_5
  • Test #8 - Conda dep had pinned version number: r-pillar=1.4.2
  • Test #8 - Conda dep had pinned version number: r-pkgconfig=2.0.3
  • Test #8 - Conda package is the latest available: r-pkgconfig=2.0.3
  • Test #8 - Conda dep had pinned version number: r-plyr=1.8.4
  • Test #8 - Conda dep had pinned version number: r-r6=2.4.0
  • Test #8 - Conda dep had pinned version number: r-rcolorbrewer=1.1_2
  • Test #8 - Conda package is the latest available: r-rcolorbrewer=1.1_2
  • Test #8 - Conda dep had pinned version number: r-rcpp=1.0.2
  • Test #8 - Conda dep had pinned version number: r-rcppparallel=4.4.4
  • Test #8 - Conda dep had pinned version number: r-rcurl=1.95_4.12
  • Test #8 - Conda dep had pinned version number: r-reshape2=1.4.3
  • Test #8 - Conda dep had pinned version number: r-rlang=0.4.1
  • Test #8 - Conda dep had pinned version number: r-scales=1.0.0
  • Test #8 - Conda dep had pinned version number: r-snow=0.4_3
  • Test #8 - Conda package is the latest available: r-snow=0.4_3
  • Test #8 - Conda dep had pinned version number: r-stringi=1.4.3
  • Test #8 - Conda dep had pinned version number: r-stringr=1.4.0
  • Test #8 - Conda package is the latest available: r-stringr=1.4.0
  • Test #8 - Conda dep had pinned version number: r-tibble=2.1.3
  • Test #8 - Conda dep had pinned version number: r-utf8=1.1.4
  • Test #8 - Conda package is the latest available: r-utf8=1.1.4
  • Test #8 - Conda dep had pinned version number: r-vctrs=0.2.0
  • Test #8 - Conda dep had pinned version number: r-vegan=2.5_6
  • Test #8 - Conda dep had pinned version number: r-viridislite=0.3.0
  • Test #8 - Conda package is the latest available: r-viridislite=0.3.0
  • Test #8 - Conda dep had pinned version number: r-withr=2.1.2
  • Test #8 - Conda dep had pinned version number: r-zeallot=0.1.0
  • Test #8 - Conda package is the latest available: r-zeallot=0.1.0
  • Test #8 - Conda dep had pinned version number: raxml=8.2.12
  • Test #8 - Conda package is the latest available: raxml=8.2.12
  • Test #8 - Conda dep had pinned version number: readline=8.0
  • Test #8 - Conda package is the latest available: readline=8.0
  • Test #8 - Conda dep had pinned version number: requests=2.22.0
  • Test #8 - Conda dep had pinned version number: conda-forge::scikit-bio=0.5.5
  • Test #8 - Conda dep had pinned version number: scikit-learn=0.21.2
  • Test #8 - Conda dep had pinned version number: scipy=1.3.1
  • Test #8 - Conda dep had pinned version number: seaborn=0.9.0
  • Test #8 - Conda dep had pinned version number: send2trash=1.5.0
  • Test #8 - Conda package is the latest available: send2trash=1.5.0
  • Test #8 - Conda dep had pinned version number: sepp=4.3.10
  • Test #8 - Conda package is the latest available: sepp=4.3.10
  • Test #8 - Conda dep had pinned version number: setuptools=41.6.0
  • Test #8 - Conda dep had pinned version number: sina=1.6.0
  • Test #8 - Conda dep had pinned version number: sip=4.19.8
  • Test #8 - Conda dep had pinned version number: six=1.12.0
  • Test #8 - Conda dep had pinned version number: sortmerna=2.0
  • Test #8 - Conda dep had pinned version number: sqlite=3.30.1
  • Test #8 - Conda dep had pinned version number: statsmodels=0.10.1
  • Test #8 - Conda dep had pinned version number: tbb=2019.9
  • Test #8 - Conda dep had pinned version number: terminado=0.8.2
  • Test #8 - Conda dep had pinned version number: testpath=0.4.2
  • Test #8 - Conda dep had pinned version number: tk=8.6.9
  • Test #8 - Conda dep had pinned version number: tktable=2.10
  • Test #8 - Conda package is the latest available: tktable=2.10
  • Test #8 - Conda dep had pinned version number: tornado=6.0.3
  • Test #8 - Conda dep had pinned version number: traitlets=4.3.3
  • Test #8 - Conda dep had pinned version number: conda-forge::tzlocal=2.0.0
  • Test #8 - Conda dep had pinned version number: unifrac=0.10.0
  • Test #8 - Conda dep had pinned version number: urllib3=1.25.6
  • Test #8 - Conda dep had pinned version number: vsearch=2.7.0
  • Test #8 - Conda dep had pinned version number: wcwidth=0.1.7
  • Test #8 - Conda dep had pinned version number: webencodings=0.5.1
  • Test #8 - Conda package is the latest available: webencodings=0.5.1
  • Test #8 - Conda dep had pinned version number: wheel=0.33.6
  • Test #8 - Conda dep had pinned version number: widgetsnbextension=3.5.1
  • Test #8 - Conda package is the latest available: widgetsnbextension=3.5.1
  • Test #8 - Conda dep had pinned version number: xopen=0.8.4
  • Test #8 - Conda dep had pinned version number: xorg-fixesproto=5.0
  • Test #8 - Conda package is the latest available: xorg-fixesproto=5.0
  • Test #8 - Conda dep had pinned version number: xorg-inputproto=2.3.2
  • Test #8 - Conda package is the latest available: xorg-inputproto=2.3.2
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  • Test #8 - Conda package is the latest available: xorg-kbproto=1.0.7
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  • Test #8 - Conda package is the latest available: xorg-libice=1.0.10
  • Test #8 - Conda dep had pinned version number: xorg-libsm=1.2.3
  • Test #8 - Conda package is the latest available: xorg-libsm=1.2.3
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  • Test #8 - Conda dep had pinned version number: xorg-libxau=1.0.9
  • Test #8 - Conda package is the latest available: xorg-libxau=1.0.9
  • Test #8 - Conda dep had pinned version number: xorg-libxdmcp=1.1.3
  • Test #8 - Conda package is the latest available: xorg-libxdmcp=1.1.3
  • Test #8 - Conda dep had pinned version number: xorg-libxext=1.3.4
  • Test #8 - Conda package is the latest available: xorg-libxext=1.3.4
  • Test #8 - Conda dep had pinned version number: xorg-libxfixes=5.0.3
  • Test #8 - Conda package is the latest available: xorg-libxfixes=5.0.3
  • Test #8 - Conda dep had pinned version number: xorg-libxi=1.7.10
  • Test #8 - Conda package is the latest available: xorg-libxi=1.7.10
  • Test #8 - Conda dep had pinned version number: xorg-libxrender=0.9.10
  • Test #8 - Conda package is the latest available: xorg-libxrender=0.9.10
  • Test #8 - Conda dep had pinned version number: xorg-libxtst=1.2.3
  • Test #8 - Conda package is the latest available: xorg-libxtst=1.2.3
  • Test #8 - Conda dep had pinned version number: xorg-recordproto=1.14.2
  • Test #8 - Conda package is the latest available: xorg-recordproto=1.14.2
  • Test #8 - Conda dep had pinned version number: xorg-renderproto=0.11.1
  • Test #8 - Conda package is the latest available: xorg-renderproto=0.11.1
  • Test #8 - Conda dep had pinned version number: xorg-xextproto=7.3.0
  • Test #8 - Conda package is the latest available: xorg-xextproto=7.3.0
  • Test #8 - Conda dep had pinned version number: xorg-xproto=7.0.31
  • Test #8 - Conda package is the latest available: xorg-xproto=7.0.31
  • Test #8 - Conda dep had pinned version number: xz=5.2.4
  • Test #8 - Conda dep had pinned version number: yaml=0.1.7
  • Test #8 - Conda dep had pinned version number: zeromq=4.3.2
  • Test #8 - Conda dep had pinned version number: zipp=0.6.0
  • Test #8 - Conda dep had pinned version number: zlib=1.2.11
  • Test #8 - Conda package is the latest available: zlib=1.2.11
  • Test #8 - Conda dep had pinned version number: zstd=1.4.3
  • Test #9 - Found all expected strings in Dockerfile file
  • Test #12 - Name adheres to nf-core convention
  • Test #13 - Did not find any cookiecutter template strings (64 files)
  • Test #14 - Schema lint passed
  • Test #14 - Schema title + description lint passed
  • Test #15 - Schema matched params returned from nextflow config

Run details:

  • nf-core/tools version 1.12.1
  • Run at 2021-02-04 16:05:17
@ewels ewels added the bug Something isn't working label Feb 4, 2021
@erikrikarddaniel
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erikrikarddaniel commented Feb 5, 2021 •
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Thanks @ewels,

I've seen this testing of full datasets mentioned. I suppose that's something to prepare. I'll make an issue for that. There is already one: #215.

The Conda warnings are probably because we're still using a pretty old version of QIIME2, right @d4straub? There's an issue for that too: #214.

I'll make an issue of the README.md thing too.

With that, I'm closing this.

@d4straub
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d4straub commented Feb 5, 2021

All the warnings fall into 3 categories:

  • outdated conda packages -> we have such a problematic environment that I only update those when I see a clear benefit
  • AWS full tests -> I opened an issue already, but this isn't high priority for me.
  • README.md -> this is a reminder that I haven't added the citations for the full pipeline. I actually was thinking about generating a method section automatically depending on what processes are run, but again, this isn't highest priority for me.

Essentially, I intentionally kept the "TODO" strings to remind myself and any anybody else who might look into it.

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@ewels @erikrikarddaniel @d4straub