docs: Add tab for known ARETE issues #181
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Signed-off-by: jvfe <jvfecav@gmail.com>
jvfe
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Feb 5, 2024
Signed-off-by: jvfe <jvfecav@gmail.com>
jvfe
added a commit
that referenced
this pull request
Feb 5, 2024
* RSPR approx and exact scripts * Add functional documentation and update support threshold * Fix rspr argument * Use clustering information from rSPR * Generate cluster heatmap * Generate group heatmaps * Create new grouping strategy * Update manifest name in config * Fix compare group size issue * Save frequency table for dedugging * Store index with pivot csv * Convert approx rspr column to numeric for crosstab * Save approx distance as integer * Store group csv as well * Use tight limits for group size * Run approx rsrp only * Revert "Run approx rsrp only" This reverts commit 3ff4365. * print frequency table * exit after approx rspr * Only run approx rspr * Remove all logging changes * use different cmap for heatmap * Reset color map * Update heatmap figure size * Revert "Only run approx rspr" This reverts commit 271d6d3. * Remove exit in rspr * Run approx rspr in groups * update group size temporary * run rspr approx only * Fix result output parsing issue * print total length for debuging * Fix index out of bound issue * print total length for debuging * Clear temp file * Seek to top of the file before clearing * Remove debugging lines * Enable run rspr exact * Create log scale heatmaps * Generate cluster network tree * Pass min and max distances for heatmap generation * Generate range heatmap if input provided * Update sub repo config * Add execution permission to rspr scripts * feat: Add rooted reference tree to exact/heatmap inputs * Revert local execution changes for exact rspr * Debugging code for input dataframe * Fix read csv issue and add documentation * Fix local rspr path * fix: Update rspr image to 1.3.6 * Add clustering part to heatmap to generate overall clustering network * Fix cluster file name issue * refactor: Add bio.phylo to rSPR image Signed-off-by: jvfe <jvfecav@gmail.com> * feat: Add cluster_file to rSPR workflow - Adds cluster_file to RSPR_EXACT outputs - Concatenate cluster_file* in the rSPR subworkflow - Adds concatenated cluster_file.txt to RSPR_HEATMAP inputs * Fix error generating cluster network * Fix reading clusters issue * Reduce figure size to half * Use cluster probability instead of branch length * Fix cluster branch length issue * Fix extra parameter issue * Update input output paths * Fix output channels * Do not pass reference tree in parameters * feat: Add light profile to config (#180) * feat: Add light profile to config * docs: Add information about the light profile --------- Signed-off-by: jvfe <jvfecav@gmail.com> * refactor: Add process_long to evolccm Signed-off-by: jvfe <jvfecav@gmail.com> * docs: Add efaecium paper to citations.md * docs: Add tab for known ARETE issues (#181) Signed-off-by: jvfe <jvfecav@gmail.com> * docs: Add note about the RSPR_HEATMAP issue Signed-off-by: jvfe <jvfecav@gmail.com> * docs: Add basic contribution guidelines Signed-off-by: jvfe <jvfecav@gmail.com> * docs: Add logo and favicon Signed-off-by: jvfe <jvfecav@gmail.com> * refactor: Remove old unused nf-core functions (#182) * refactor: Remove unused nf-core functions Signed-off-by: jvfe <jvfecav@gmail.com> * fix: Remove missing functions in RGI module Signed-off-by: jvfe <jvfecav@gmail.com> --------- Signed-off-by: jvfe <jvfecav@gmail.com> * refactor: Add rspr and evolccm to annotation entry (#183) Signed-off-by: jvfe <jvfecav@gmail.com> * docs: Update arete logo Signed-off-by: jvfe <jvfecav@gmail.com> * docs: Update poppunk website url Signed-off-by: jvfe <jvfecav@gmail.com> * docs: Make it clear that dynamics tools are optional Signed-off-by: jvfe <jvfecav@gmail.com> * docs(output): Add not about modules not included in report Signed-off-by: jvfe <jvfecav@gmail.com> * docs: Add link to full documentation Signed-off-by: jvfe <jvfecav@gmail.com> * docs: Add a command that runs all subworkflows * docs(usage): Add note about storage requirements Signed-off-by: jvfe <jvfecav@gmail.com> * docs: Fix header in readme * refactor: Add 1.0 threshold to subsetting heatmap (#184) * refactor: Reduce number of tools on ci test Signed-off-by: jvfe <jvfecav@gmail.com> * refactor: Remove group outputs from rspr exact Signed-off-by: jvfe <jvfecav@gmail.com> * fix: Remove old fork name Signed-off-by: jvfe <jvfecav@gmail.com> --------- Signed-off-by: jvfe <jvfecav@gmail.com> Co-authored-by: KARTIK KAKADIYA <20909285+ktkakadiya@users.noreply.github.com> Co-authored-by: ktkakadiya <99840261+ktkakadiya@users.noreply.github.com>
jvfe
added a commit
that referenced
this pull request
Apr 16, 2024
Signed-off-by: jvfe <jvfecav@gmail.com>
jvfe
added a commit
that referenced
this pull request
Apr 16, 2024
* RSPR approx and exact scripts * Add functional documentation and update support threshold * Fix rspr argument * Use clustering information from rSPR * Generate cluster heatmap * Generate group heatmaps * Create new grouping strategy * Update manifest name in config * Fix compare group size issue * Save frequency table for dedugging * Store index with pivot csv * Convert approx rspr column to numeric for crosstab * Save approx distance as integer * Store group csv as well * Use tight limits for group size * Run approx rsrp only * Revert "Run approx rsrp only" This reverts commit 3ff4365. * print frequency table * exit after approx rspr * Only run approx rspr * Remove all logging changes * use different cmap for heatmap * Reset color map * Update heatmap figure size * Revert "Only run approx rspr" This reverts commit 271d6d3. * Remove exit in rspr * Run approx rspr in groups * update group size temporary * run rspr approx only * Fix result output parsing issue * print total length for debuging * Fix index out of bound issue * print total length for debuging * Clear temp file * Seek to top of the file before clearing * Remove debugging lines * Enable run rspr exact * Create log scale heatmaps * Generate cluster network tree * Pass min and max distances for heatmap generation * Generate range heatmap if input provided * Update sub repo config * Add execution permission to rspr scripts * feat: Add rooted reference tree to exact/heatmap inputs * Revert local execution changes for exact rspr * Debugging code for input dataframe * Fix read csv issue and add documentation * Fix local rspr path * fix: Update rspr image to 1.3.6 * Add clustering part to heatmap to generate overall clustering network * Fix cluster file name issue * refactor: Add bio.phylo to rSPR image Signed-off-by: jvfe <jvfecav@gmail.com> * feat: Add cluster_file to rSPR workflow - Adds cluster_file to RSPR_EXACT outputs - Concatenate cluster_file* in the rSPR subworkflow - Adds concatenated cluster_file.txt to RSPR_HEATMAP inputs * Fix error generating cluster network * Fix reading clusters issue * Reduce figure size to half * Use cluster probability instead of branch length * Fix cluster branch length issue * Fix extra parameter issue * Update input output paths * Fix output channels * Do not pass reference tree in parameters * feat: Add light profile to config (#180) * feat: Add light profile to config * docs: Add information about the light profile --------- Signed-off-by: jvfe <jvfecav@gmail.com> * refactor: Add process_long to evolccm Signed-off-by: jvfe <jvfecav@gmail.com> * docs: Add efaecium paper to citations.md * docs: Add tab for known ARETE issues (#181) Signed-off-by: jvfe <jvfecav@gmail.com> * docs: Add note about the RSPR_HEATMAP issue Signed-off-by: jvfe <jvfecav@gmail.com> * docs: Add basic contribution guidelines Signed-off-by: jvfe <jvfecav@gmail.com> * docs: Add logo and favicon Signed-off-by: jvfe <jvfecav@gmail.com> * refactor: Remove old unused nf-core functions (#182) * refactor: Remove unused nf-core functions Signed-off-by: jvfe <jvfecav@gmail.com> * fix: Remove missing functions in RGI module Signed-off-by: jvfe <jvfecav@gmail.com> --------- Signed-off-by: jvfe <jvfecav@gmail.com> * refactor: Add rspr and evolccm to annotation entry (#183) Signed-off-by: jvfe <jvfecav@gmail.com> * docs: Update arete logo Signed-off-by: jvfe <jvfecav@gmail.com> * docs: Update poppunk website url Signed-off-by: jvfe <jvfecav@gmail.com> * docs: Make it clear that dynamics tools are optional Signed-off-by: jvfe <jvfecav@gmail.com> * docs(output): Add not about modules not included in report Signed-off-by: jvfe <jvfecav@gmail.com> * docs: Add link to full documentation Signed-off-by: jvfe <jvfecav@gmail.com> * docs: Add a command that runs all subworkflows * docs(usage): Add note about storage requirements Signed-off-by: jvfe <jvfecav@gmail.com> * docs: Fix header in readme * refactor: Add 1.0 threshold to subsetting heatmap (#184) * refactor: Reduce number of tools on ci test Signed-off-by: jvfe <jvfecav@gmail.com> * refactor: Remove group outputs from rspr exact Signed-off-by: jvfe <jvfecav@gmail.com> * fix: Remove old fork name Signed-off-by: jvfe <jvfecav@gmail.com> --------- Signed-off-by: jvfe <jvfecav@gmail.com> Co-authored-by: KARTIK KAKADIYA <20909285+ktkakadiya@users.noreply.github.com> Co-authored-by: ktkakadiya <99840261+ktkakadiya@users.noreply.github.com>
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Signed-off-by: jvfe jvfecav@gmail.com